P03314 (POLG_YEFV1) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names	Recommended name: Genome polyprotein Cleaved into the following 14 chains: Capsid protein C Alternative name(s): Core protein prM Peptide pr Small envelope protein M Alternative name(s): Matrix protein Envelope protein E Non-structural protein 1 Short name=NS1 Non-structural protein 2A Short name=NS2A Non-structural protein 2A-alpha Short name=NS2A-alpha Serine protease subunit NS2B Alternative name(s): Flavivirin protease NS2B regulatory subunit Non-structural protein 2B Serine protease NS3 EC=3.4.21.91 EC=3.6.1.15 EC=3.6.4.13 Alternative name(s): Flavivirin protease NS3 catalytic subunit Non-structural protein 3 Non-structural protein 4A Short name=NS4A Peptide 2k Non-structural protein 4B Short name=NS4B RNA-directed RNA polymerase NS5 EC=2.1.1.56 EC=2.1.1.57 EC=2.7.7.48 Alternative name(s): Non-structural protein 5
Organism	Yellow fever virus (strain 17D vaccine) (YFV) [Reference proteome]
Taxonomic identifier	11090 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Flaviviridae › Flavivirus › Yellow fever virus group › Yellow fever virus
Virus host	Aedes aegypti (Yellowfever mosquito) (Culex aegypti) [TaxID: 7159] Aedes luteocephalus (Mosquito) [TaxID: 299629] Aedes simpsoni [TaxID: 7161] Homo sapiens (Human) [TaxID: 9606] Simiiformes [TaxID: 314293]

Protein attributes

Sequence length	3411 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Capsid protein C self-assembles to form an icosahedral capsid about 30 nm in diameter. The capsid encapsulates the genomic RNA By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 prM acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is matured in the last step of virion assembly, presumably to avoid catastrophic activation of the viral fusion peptide induced by the acidic pH of the trans-Golgi network. After cleavage by host furin, the pr peptide is released in the extracellular medium and small envelope protein M and envelope protein E homodimers are dissociated By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 Non-structural protein 1 is involved in virus replication and regulation of the innate immune response By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 Non-structural protein 2A may be involved viral RNA replication and capsid assembly Potential. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 Non-structural protein 2B is a required cofactor for the serine protease function of NS3 By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 Serine protease NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS2B, performs its autocleavage and cleaves the polyprotein at dibasic sites in the cytoplasm: C-prM, NS2A-NS2B, NS2B-NS3, NS3-NS4A, NS4A-2K and NS4B-NS5. NS3 RNA helicase binds RNA and unwinds dsRNA in the 3' to 5' direction By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 Non-structural protein 4A induces host endoplasmic reticulum membrane rearrangements leading to the formation of virus-induced membranous vesicles hosting the dsRNA and polymerase, functioning as a replication complex. NS4A might also regulate the ATPase activity of the NS3 helicase By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 Peptide 2k functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 Non-structural protein 4B inhibits interferon (IFN)-induced host STAT1 phosphorylation and nuclear translocation, thereby preventing the establishment of cellular antiviral state by blocking the IFN-alpha/beta pathway By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29 RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome, and performs the capping of genomes in the cytoplasm. NS5 methylates viral RNA cap at guanine N-7 and ribose 2'-O positions. Besides its role in genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway By similarity. Ref.14 Ref.18 Ref.27 Ref.28 Ref.29
Catalytic activity	Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala. Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). NTP + H2O = NDP + phosphate. ATP + H2O = ADP + phosphate. S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppR-RNA. S-adenosyl-L-methionine + m7G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppRm-RNA.
Subunit structure	Capsid protein C forms homodimers. prM and envelope protein E form heterodimers in the endoplasmic reticulum and Golgi. In immature particles, there are 60 icosaedrally organized trimeric spikes on the surface. Each spike consists of three heterodimers of envelope protein M precursor (prM) and envelope protein E. NS1 forms homodimers as well as homohexamers when secreted. NS1 may interact with NS4A. NS3 and NS2B form a heterodimer. NS3 is the catalytic subunit, whereas NS2B strongly stimulates the latter, acting as a cofactor. In the absence of the NS2B, NS3 protease is unfolded and inactive. NS3 interacts with unphosphorylated NS5; this interaction stimulates NS5 guanylyltransferase activity By similarity. Ref.20 Ref.25
Subcellular location	Capsid protein C: Virion Potential Ref.26. Peptide pr: Secreted. Small envelope protein M: Virion membrane; Multi-pass membrane protein Potential. Host endoplasmic reticulum membrane; Multi-pass membrane protein Potential Ref.26. Envelope protein E: Virion membrane; Multi-pass membrane protein Potential. Host endoplasmic reticulum membrane; Multi-pass membrane protein Potential Ref.26. Non-structural protein 1: Secreted. Host endoplasmic reticulum membrane; Peripheral membrane protein; Lumenal side Ref.26. Non-structural protein 2A-alpha: Host endoplasmic reticulum membrane; Multi-pass membrane protein Potential Ref.26. Non-structural protein 2A: Host endoplasmic reticulum membrane; Multi-pass membrane protein Potential Ref.26. Serine protease subunit NS2B: Host endoplasmic reticulum membrane; Peripheral membrane protein; Cytoplasmic side Ref.26. Serine protease NS3: Host endoplasmic reticulum membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Note: Remains non-covalently associated to NS3 protease By similarity. Ref.26 Non-structural protein 4A: Host endoplasmic reticulum membrane; Multi-pass membrane protein By similarity Ref.26. Note: Located in RE-associated vesicles hosting the replication complex. Ref.26 Non-structural protein 4B: Host endoplasmic reticulum membrane; Multi-pass membrane protein By similarity Ref.26. RNA-directed RNA polymerase NS5: Host endoplasmic reticulum membrane; Peripheral membrane protein; Cytoplasmic side By similarity. Host nucleus By similarity. Note: Located in RE-associated vesicles hosting the replication complex. Ref.26
Domain	Transmembrane domains of the small envelope protein M and envelope protein E contains an endoplasmic reticulum retention signals.
Post-translational modification	Specific enzymatic cleavages in vivo yield mature proteins. The nascent protein C contains a C-terminal hydrophobic domain that act as a signal sequence for translocation of prM into the lumen of the ER. Mature protein C is cleaved at a site upstream of this hydrophobic domain by NS3. prM is cleaved in post-Golgi vesicles by a host furin, releasing the mature small envelope protein M, and peptide pr. Non-structural protein 2A-alpha, a C-terminally truncated form of non-structural protein 2A, results from partial cleavage by NS3. Specific enzymatic cleavages in vivo yield mature proteins Peptide 2K acts as a signal sequence and is removed from the N-terminus of NS4B by the host signal peptidase in the ER lumen. Signal cleavage at the 2K-4B site requires a prior NS3 protease-mediated cleavage at the 4A-2K site By similarity. Ref.13 RNA-directed RNA polymerase NS5 is phosphorylated on serines residues. This phosphorylation may trigger NS5 nuclear localization. Ref.19 Envelope protein E and non-structural protein 1 are N-glycosylated.
Sequence similarities	In the N-terminal section; belongs to the class I-like SAM-binding methyltransferase superfamily. mRNA cap 0-1 NS5-type methyltransferase family. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain. Contains 1 mRNA cap 0-1 NS5-type MT domain. Contains 1 peptidase S7 domain. Contains 1 RdRp catalytic domain.

Ontologies

Keywords
Biological process	Activation of host autophagy by virus Clathrin-mediated endocytosis of virus by host Fusion of virus membrane with host endosomal membrane Fusion of virus membrane with host membrane Host-virus interaction Inhibition of host innate immune response by virus Inhibition of host interferon signaling pathway by virus Transcription Transcription regulation Viral RNA replication Viral attachment to host cell Viral immunoevasion Viral penetration into host cytoplasm Virus endocytosis by host Virus entry into host cell mRNA capping mRNA processing
Cellular component	Host endoplasmic reticulum Host membrane Host nucleus Membrane Secreted Viral envelope protein Virion
Domain	Transmembrane Transmembrane helix
Ligand	ATP-binding Metal-binding Nucleotide-binding RNA-binding S-adenosyl-L-methionine
Molecular function	Capsid protein Helicase Hydrolase Methyltransferase Nucleotidyltransferase Protease RNA-directed RNA polymerase Serine protease Transferase
PTM	Cleavage on pair of basic residues Disulfide bond Glycoprotein Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Multifunctional enzyme Reference proteome
Gene Ontology (GO)
Biological_process	RNA (guanine-N7)-methylation Inferred from electronic annotation. Source: GOC induction by virus of host autophagy Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host type I interferon-mediated signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW viral attachment to host cell Inferred from electronic annotation. Source: UniProtKB-KW viral entry into host cell via clathrin-mediated endocytosis Inferred from electronic annotation. Source: UniProtKB-KW viral genome replication Inferred from electronic annotation. Source: InterPro
Cellular_component	host cell endoplasmic reticulum membrane Inferred from electronic annotation. Source: UniProtKB-SubCell host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW viral capsid Inferred from electronic annotation. Source: UniProtKB-KW viral envelope Inferred from electronic annotation. Source: UniProtKB-KW virion membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro RNA helicase activity Inferred from electronic annotation. Source: InterPro RNA-directed RNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW double-stranded RNA binding Inferred from electronic annotation. Source: InterPro mRNA (guanine-N7-)-methyltransferase activity Inferred from electronic annotation. Source: EC mRNA (nucleoside-2'-O-)-methyltransferase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW serine-type endopeptidase activity Inferred from electronic annotation. Source: InterPro serine-type exopeptidase activity Inferred from electronic annotation. Source: InterPro structural molecule activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 3411

3411

Genome polyprotein

PRO_0000405153

Chain

1 – 101

101

Capsid protein C By similarity

PRO_0000037754

Propeptide

102 – 121

20

ER anchor for the protein C, removed in mature form by serine protease NS3

PRO_0000261384

Chain

122 – 285

164

prM By similarity

PRO_0000261385

Chain

122 – 210

89

Peptide pr By similarity

PRO_0000037755

Chain

211 – 285

75

Small envelope protein M By similarity

PRO_0000037756

Chain

286 – 778

493

Envelope protein E By similarity

PRO_0000037757

Chain

779 – 1130

352

Non-structural protein 1 By similarity

PRO_0000037758

Chain

1131 – 1354

224

Non-structural protein 2A By similarity

PRO_0000037759

Chain

1131 – 1320

190

Non-structural protein 2A-alpha By similarity

PRO_0000261386

Chain

1355 – 1484

130

Serine protease subunit NS2B By similarity

PRO_0000037760

Chain

1485 – 2107

623

Serine protease NS3 By similarity

PRO_0000037761

Chain

2108 – 2233

126

Non-structural protein 4A By similarity

PRO_0000037762

Peptide

2234 – 2256

23

Peptide 2k

PRO_0000261387

Chain

2257 – 2506

250

Non-structural protein 4B By similarity

PRO_0000037763

Chain

2507 – 3411

905

RNA-directed RNA polymerase NS5 By similarity

PRO_0000037764

Regions

Topological domain

1 – 104

104

Cytoplasmic Potential

Transmembrane

105 – 125

21

Helical; Potential

Topological domain

126 – 244

119

Extracellular Potential

Transmembrane

245 – 265

21

Helical; Potential

Topological domain

266 – 270

5

Cytoplasmic Potential

Transmembrane

271 – 285

15

Helical; Potential

Topological domain

286 – 730

445

Extracellular Potential

Intramembrane

731 – 751

21

Helical; Potential

Topological domain

752 – 757

6

Extracellular Potential

Intramembrane

758 – 778

21

Helical; Potential

Topological domain

779 – 1130

352

Extracellular Potential

Transmembrane

1131 – 1151

21

Helical; Potential

Topological domain

1152 – 1160

9

Cytoplasmic Potential

Transmembrane

1161 – 1181

21

Helical; Potential

Topological domain

1182 – 1201

20

Lumenal Potential

Transmembrane

1202 – 1222

21

Helical; Potential

Topological domain

1223 – 1231

9

Cytoplasmic Potential

Transmembrane

1232 – 1252

21

Helical; Potential

Topological domain

1253 – 1262

10

Lumenal Potential

Transmembrane

1263 – 1285

23

Helical; Potential

Topological domain

1286 – 1355

70

Cytoplasmic Potential

Transmembrane

1356 – 1376

21

Helical; Potential

Topological domain

1377 – 1378

2

Lumenal Potential

Transmembrane

1379 – 1399

21

Helical; Potential

Topological domain

1400 – 1456

57

Cytoplasmic Potential

Intramembrane

1457 – 1477

21

Helical; Potential

Topological domain

1478 – 2157

680

Cytoplasmic Potential

Transmembrane

2158 – 2178

21

Helical; Potential

Topological domain

2179 – 2186

8

Lumenal Potential

Intramembrane

2187 – 2207

21

Helical; Potential

Topological domain

2208 – 2209

2

Lumenal Potential

Transmembrane

2210 – 2230

21

Helical; Potential

Topological domain

2231 – 2241

11

Cytoplasmic Potential

Transmembrane

2242 – 2262

21

Helical; Note=Signal for NS4B; Potential

Topological domain

2263 – 2293

31

Lumenal Potential

Intramembrane

2294 – 2314

21

Helical; Potential

Topological domain

2315 – 2338

24

Lumenal Potential

Intramembrane

2339 – 2359

21

Helical; Potential

Topological domain

2360

1

Lumenal Potential

Transmembrane

2361 – 2380

20

Helical; Potential

Topological domain

2381 – 2421

41

Cytoplasmic Potential

Transmembrane

2422 – 2442

21

Helical; Potential

Topological domain

2443 – 2445

3

Lumenal Potential

Transmembrane

2446 – 2466

21

Helical; Potential

Topological domain

2467 – 3411

945

Cytoplasmic Potential

Domain

1485 – 1665

181

Peptidase S7

Domain

1669 – 1825

157

Helicase ATP-binding

Domain

1820 – 1997

178

Helicase C-terminal

Domain

2507 – 2771

265

mRNA cap 0-1 NS5-type MT

Domain

3035 – 3187

153

RdRp catalytic

Nucleotide binding

1682 – 1689

8

ATP Potential

Region

30 – 74

45

Hydrophobic; homodimerization of capsid protein C By similarity

Region

383 – 396

14

Involved in fusion

Region

1407 – 1446

40

Interacts with and activates NS3 protease By similarity

Motif

1773 – 1776

4

DEAH box

Motif

2878 – 2911

34

Nuclear localization signal By similarity

Compositional bias

2656 – 2660

5

Poly-Ser

Sites

Active site

1537

1

Charge relay system; for serine protease NS3 activity

Active site

1561

1

Charge relay system; for serine protease NS3 activity

Active site

1622

1

Charge relay system; for serine protease NS3 activity

Binding site

2519

1

mRNA cap

Binding site

2522

1

mRNA cap; via carbonyl oxygen

Binding site

2523

1

mRNA cap

Binding site

2525

1

mRNA cap; via carbonyl oxygen

Binding site

2534

1

mRNA cap

Binding site

2562

1

S-adenosyl-L-methionine By similarity

Binding site

2592

1

S-adenosyl-L-methionine; via carbonyl oxygen By similarity

Binding site

2593

1

S-adenosyl-L-methionine; via carbonyl oxygen By similarity

Binding site

2610

1

S-adenosyl-L-methionine By similarity

Binding site

2611

1

S-adenosyl-L-methionine; via carbonyl oxygen By similarity

Binding site

2637

1

S-adenosyl-L-methionine By similarity

Binding site

2638

1

S-adenosyl-L-methionine; via carbonyl oxygen By similarity

Binding site

2656

1

mRNA cap

Binding site

2719

1

mRNA cap

Binding site

2721

1

mRNA cap

Binding site

2726

1

S-adenosyl-L-methionine By similarity

Site

101 – 102

2

Cleavage; by viral protease NS3 Potential

Site

121 – 122

2

Cleavage; by host signal peptidase By similarity

Site

210 – 211

2

Cleavage; by host furin Potential

Site

285 – 286

2

Cleavage; by host signal peptidase Potential

Site

778 – 779

2

Cleavage; by host signal peptidase Potential

Site

1130 – 1131

2

Cleavage; by host Potential

Site

1354 – 1355

2

Cleavage; by viral protease NS3 Potential

Site

1484 – 1485

2

Cleavage; by autolysis Potential

Site

2107 – 2108

2

Cleavage; by autolysis Potential

Site

2233 – 2234

2

Cleavage; by viral protease NS3 Potential

Site

2256 – 2257

2

Cleavage; by host signal peptidase Potential

Site

2506 – 2507

2

Cleavage; by viral protease NS3 Potential

Site

2530

1

mRNA cap binding

Site

2567

1

Essential for 2'-O-methyltransferase activity By similarity

Site

2652

1

Essential for 2'-O-methyltransferase and N-7 methyltransferase activity By similarity

Site

2653

1

S-adenosyl-L-methionine binding By similarity

Site

2688

1

Essential for 2'-O-methyltransferase activity By similarity

Site

2724

1

Essential for 2'-O-methyltransferase activity By similarity

Amino acid modifications

Glycosylation

134

1

N-linked (GlcNAc...); by host Potential

Glycosylation

150

1

N-linked (GlcNAc...); by host Potential

Glycosylation

908

1

N-linked (GlcNAc...); by host Potential

Glycosylation

986

1

N-linked (GlcNAc...); by host Potential

Disulfide bond

288 ↔ 315

By similarity

Disulfide bond

345 ↔ 401

By similarity

Disulfide bond

359 ↔ 390

By similarity

Disulfide bond

377 ↔ 406

By similarity

Disulfide bond

467 ↔ 568

By similarity

Disulfide bond

585 ↔ 615

By similarity

Natural variations

Natural variant

341

1

V → A in strain: Isolate Brazil/YF-VAVD/75 vaccine and Isolate 17DD vaccine.

Natural variant

438

1

N → T in strain: Isolate 17D-204-USA HONG1 vaccine, Isolate 17D-204-USA HONG2 vaccine and Isolate 17D-204-USA HONG3 vaccine.

Natural variant

440

1

D → S in strain: Isolate 17DD vaccine.

Natural variant

610

1

S → P in strain: Isolate Brazil/YF-VAVD/75 vaccine and Isolate 17DD vaccine.

Natural variant

629

1

I → V in strain: Isolate Brazil/YF-VAVD/75 vaccine.

Natural variant

701

1

T → V in strain: Isolate 17DD vaccine.

Natural variant

744

1

A → V in strain: Isolate 17D-204-South Africa vaccine large plaque variant.

Natural variant

764

1

L → M in strain: Isolate 17D-204-South Africa vaccine large plaque variant.

Natural variant

1299

1

F → L in strain: Isolate Brazil/YF-VAVD/75 vaccine and Isolate 17DD vaccine.

Natural variant

1666

1

Q → R in strain: Isolate 17DD vaccine.

Natural variant

1669

1

P → S in strain: Isolate Brazil/YF-VAVD/75 vaccine.

Natural variant

1679

1

V → I in strain: Isolate Brazil/YF-VAVD/75 vaccine and Isolate 17DD vaccine.

Natural variant

2214

1

V → I in strain: Isolate 17D-204-USA HONG1 vaccine, Isolate 17D-204-USA HONG2 vaccine, Isolate 17D-204-USA HONG3 vaccine, Isolate Spain/AVD2791-93F/04 vaccine, Isolate Brazil/YF-VAVD/75 vaccine, Isolate 17DD vaccine and Isolate Pasteur 17D-204 vaccine.

Natural variant

2277

1

P → S in strain: Isolate Brazil/YF-VAVD/75 vaccine.

Natural variant

2401

1

E → K in strain: Isolate 17D-204-South Africa vaccine large plaque variant, Isolate 17D-204-South Africa vaccine medium plaque variant, Isolate 17D-204-South Africa vaccine, Isolate 17D-204-USA HONG1 vaccine, Isolate 17D-204-USA HONG2 vaccine, Isolate 17D-204-USA HONG3 vaccine, Isolate Brazil/YF-VAVD/75 vaccine, Isolate Spain/AVD2791-93F/04 vaccine, Isolate 17DD vaccine and Isolate Pasteur 17D-204 vaccine.

Natural variant

2460

1

L → S in strain: Isolate 17D-204-USA HONG vaccine1, Isolate 17D-204-USA HONG2 vaccine and Isolate 17D-204-USA HONG3 vaccine.

Natural variant

2528

1

R → Q in strain: Isolate Brazil/YF-VAVD/75 vaccine and Isolate 17DD vaccine.

Natural variant

2643

1

P → S in strain: Isolate 17D-204-South Africa vaccine medium plaque variant.

Natural variant

2661

1

V → I in strain: Isolate Brazil/YF-VAVD/75 vaccine.

Natural variant

2897

1

N → S in strain: Isolate Brazil/YF-VAVD/75 vaccine and Isolate 17DD vaccine.

Natural variant

3110

1

G → R in strain: Isolate 17D-204-USA HONG2 vaccine.

Natural variant

3135

1

M → N in strain: Isolate Brazil/YF-VAVD/75 vaccine.

Natural variant

3163

1

D → N in strain: Isolate 17D-204-South Africa vaccine large plaque variant, Isolate 17D-204-South Africa vaccine medium plaque variant, Isolate 17D-204-South Africa vaccine, Isolate 17D-204-USA HONG1 vaccine, Isolate 17D-204-USA HONG2 vaccine, Isolate 17D-204-USA HONG3 vaccine, Isolate Brazil/YF-VAVD/75 vaccine, Isolate Spain/AVD2791-93F/04 vaccine, Isolate 17DD vaccine and Isolate Pasteur 17D-204 vaccine.

Natural variant

3222

1

H → R in strain: Isolate Brazil/YF-VAVD/75 vaccine.

Experimental info

Mutagenesis

98 – 101

4

RKRR → AAAA: Complete loss of NS2B-NS3 cleavage.

Mutagenesis

98 – 101

4

RKRR → AKAA: Complete loss of NS2B-NS3 cleavage.

Mutagenesis

98 – 101

4

RKRR → AKRA: Reduces NS2B-NS3 cleavage efficiency.

Mutagenesis

98 – 100

3

RKR → AAA: Complete loss of NS2B-NS3 cleavage.

Mutagenesis

98 – 100

3

RKR → AKA: Complete loss of NS2B-NS3 cleavage.

Mutagenesis

98 – 99

2

RK → AA: Reduces NS2B-NS3 cleavage efficiency.

Mutagenesis

99 – 101

3

KRR → ARA: Complete loss of NS2B-NS3 cleavage. Ref.21

Mutagenesis

99 – 100

2

KR → AA: Complete loss of NS2B-NS3 cleavage.

Mutagenesis

100 – 101

2

RR → AA: Reduces NS2B-NS3 cleavage efficiency.

Mutagenesis

116 – 121

6

LLMTGG → VPQAQA: Complete loss of infectious virus production. Enhances signal peptidase cleavage in vitro of nascent protein C. Ref.22

Mutagenesis

908

1

N → A: Reduces viral RNA accumulation and NS1 secretion. Ref.16

Mutagenesis

910

1

S → A: Reduces viral RNA accumulation and NS1 secretion. Ref.16

Mutagenesis

986

1

N → A: No effect. Ref.16

Mutagenesis

988

1

T → A: No effect. Ref.16

Mutagenesis

1077

1

R → A: Blocks RNA replication. Ref.17

Mutagenesis

1319 – 1321

3

QKT → RRS: Increases NS2A-alpha processing, complete loss of NS2A. Ref.24

Mutagenesis

1319

1

Q → S: Complete loss of cleavage and NS2A alpha. Complete loss of infectivity. Ref.24

Mutagenesis

1320

1

K → E, I, Q or S: Complete loss of cleavage and NS2A-alpha processing. Complete loss of infectivity. Ref.24

Mutagenesis

1320

1

K → R: No effect on NS2A-alpha processing. Ref.24

Mutagenesis

1321

1

T → V: Complete loss of cleavage and NS2A alpha synthesis. Complete loss of infectivity. Ref.24

Mutagenesis

1351

1

F → C, I or V: Enhances NS2A-NS2B cleavage efficiency. Ref.15

Mutagenesis

1351

1

F → G: No effect on NS2A-NS2B cleavage efficiency. Ref.15

Mutagenesis

1352

1

G → A or K: Enhances NS2A-NS2B cleavage efficiency. Ref.15

Mutagenesis

1352

1

G → E or V: Reduces NS2A-NS2B cleavage efficiency. Ref.15

Mutagenesis

1353

1

R → H, K, R or T: Reduces NS2A-NS2B cleavage efficiency. Ref.15

Mutagenesis

1353

1

R → L or P: Complete loss of NS2A-NS2B cleavage. Ref.15

Mutagenesis

1354

1

R → I, N, S or T: Complete loss of NS2A-NS2B cleavage. Ref.15

Mutagenesis

1354

1

R → K: Reduces of NS2A-NS2B cleavage efficiency. Ref.15

Mutagenesis

1355

1

S → D, K, R or V: Complete loss of NS2A-NS2B cleavage. Ref.15

Mutagenesis

1355

1

S → G: Reduces of NS2A-NS2B cleavage efficiency. Ref.15

Mutagenesis

1406 – 1409

4

ELKK → ALAA: Complete loss of polyprotein cleavage. Ref.23

Mutagenesis

1537

1

H → A: Complete loss NS3 protease activity. Ref.10

Mutagenesis

1561

1

D → A or N: Complete loss NS3 protease activity. Ref.10

Mutagenesis

1622

1

S → A: Complete loss NS3 protease activity. Ref.10

Mutagenesis

1622

1

S → C: Diminishes NS3 protease activity. Ref.10

Mutagenesis

2107

1

R → A, L, M, T or V: Reduces NS4A-NS4B cleavage efficiency. Ref.12

Mutagenesis

2107

1

R → E or P: Complete loss of NS4A-NS4B cleavage. Ref.12

Mutagenesis

2107

1

R → K: No effect on NS4A-NS4B cleavage efficiency. Ref.12

Mutagenesis

2505

1

R → A, I, L, Q, S or T: No effect on NS4B-NS5 cleavage efficiency. Ref.12

Mutagenesis

2505

1

R → P: Reduces NS4B-NS5 cleavage efficiency. Ref.12

Mutagenesis

2506

1

R → E or Y: Complete loss of NS4B-NS5 cleavage. Ref.12

Mutagenesis

2506

1

R → H, N or Q: Reduces NS4B-NS5 cleavage efficiency. Ref.12

Mutagenesis

2506

1

R → K: No effect on NS4B-NS5 cleavage efficiency. Ref.12

Mutagenesis

2507

1

G → A or S: Reduces NS4B-NS5 cleavage efficiency.

Mutagenesis

2507

1

G → E, K, L, M, N or V: Reduces NS4B-NS5 cleavage efficiency.

Secondary structure

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3411

Helix Strand Turn

Details...

Beta strand

1677 – 1680

4

Turn

1688 – 1691

4

Helix

1692 – 1702

11

Beta strand

1707 – 1713

7

Helix

1714 – 1723

10

Turn

1724 – 1726

3

Beta strand

1729 – 1731

3

Beta strand

1746 – 1750

5

Helix

1751 – 1758

8

Beta strand

1760 – 1762

3

Beta strand

1768 – 1772

5

Turn

1773 – 1776

4

Helix

1780 – 1794

15

Beta strand

1799 – 1803

5

Beta strand

1821 – 1825

5

Beta strand

1834 – 1836

3

Helix

1839 – 1842

4

Beta strand

1847 – 1850

4

Helix

1854 – 1866

13

Beta strand

1871 – 1873

3

Beta strand

1876 – 1878

3

Beta strand

1892 – 1899

8

Beta strand

1909 – 1913

5

Beta strand

1916 – 1923

8

Turn

1924 – 1927

4

Beta strand

1928 – 1936

9

Helix

1939 – 1946

8

Beta strand

1958 – 1962

5

Helix

1974 – 1983

10

Helix

1989 – 1991

3

Helix

2000 – 2003

4

Beta strand

2004 – 2006

3

Turn

2008 – 2011

4

Helix

2015 – 2026

12

Helix

2032 – 2040

9

Helix

2049 – 2051

3

Helix

2056 – 2058

3

Beta strand

2069 – 2071

3

Beta strand

2077 – 2079

3

Beta strand

2083 – 2086

4

Helix

2087 – 2089

3

Beta strand

2090 – 2092

3

Helix

2093 – 2103

11

Turn

2104 – 2106

3

Helix

2514 – 2524

11

Helix

2527 – 2534

8

Beta strand

2536 – 2541

6

Helix

2544 – 2551

8

Helix

2564 – 2573

10

Beta strand

2581 – 2586

6

Helix

2592 – 2598

7

Beta strand

2603 – 2609

7

Helix

2627 – 2629

3

Beta strand

2630 – 2633

4

Turn

2638 – 2640

3

Beta strand

2647 – 2651

5

Helix

2660 – 2678

19

Turn

2679 – 2681

3

Beta strand

2683 – 2690

8

Helix

2695 – 2708

14

Beta strand

2711 – 2713

3

Beta strand

2725 – 2730

6

Helix

2735 – 2751

17

Beta strand

2757 – 2760

4

Sequences

	Sequence		Length	Mass (Da)
	P03314 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 680E0FACD23DCFA6	FASTA	3,411	379,518
	10 20 30 40 50 60 MSGRKAQGKT LGVNMVRRGV RSLSNKIKQK TKQIGNRPGP SRGVQGFIFF FLFNILTGKK 70 80 90 100 110 120 ITAHLKRLWK MLDPRQGLAV LRKVKRVVAS LMRGLSSRKR RSHDVLTVQF LILGMLLMTG 130 140 150 160 170 180 GVTLVRKNRW LLLNVTSEDL GKTFSVGTGN CTTNILEAKY WCPDSMEYNC PNLSPREEPD 190 200 210 220 230 240 DIDCWCYGVE NVRVAYGKCD SAGRSRRSRR AIDLPTHENH GLKTRQEKWM TGRMGERQLQ 250 260 270 280 290 300 KIERWFVRNP FFAVTALTIA YLVGSNMTQR VVIALLVLAV GPAYSAHCIG ITDRDFIEGV 310 320 330 340 350 360 HGGTWVSATL EQDKCVTVMA PDKPSLDISL ETVAIDRPAE VRKVCYNAVL THVKINDKCP 370 380 390 400 410 420 STGEAHLAEE NEGDNACKRT YSDRGWGNGC GLFGKGSIVA CAKFTCAKSM SLFEVDQTKI 430 440 450 460 470 480 QYVIRAQLHV GAKQENWNTD IKTLKFDALS GSQEVEFIGY GKATLECQVQ TAVDFGNSYI 490 500 510 520 530 540 AEMETESWIV DRQWAQDLTL PWQSGSGGVW REMHHLVEFE PPHAATIRVL ALGNQEGSLK 550 560 570 580 590 600 TALTGAMRVT KDTNDNNLYK LHGGHVSCRV KLSALTLKGT SYKICTDKMF FVKNPTDTGH 610 620 630 640 650 660 GTVVMQVKVS KGAPCRIPVI VADDLTAAIN KGILVTVNPI ASTNDDEVLI EVNPPFGDSY 670 680 690 700 710 720 IIVGRGDSRL TYQWHKEGSS IGKLFTQTMK GVERLAVMGD TAWDFSSAGG FFTSVGKGIH 730 740 750 760 770 780 TVFGSAFQGL FGGLNWITKV IMGAVLIWVG INTRNMTMSM SMILVGVIMM FLSLGVGADQ 790 800 810 820 830 840 GCAINFGKRE LKCGDGIFIF RDSDDWLNKY SYYPEDPVKL ASIVKASFEE GKCGLNSVDS 850 860 870 880 890 900 LEHEMWRSRA DEINAIFEEN EVDISVVVQD PKNVYQRGTH PFSRIRDGLQ YGWKTWGKNL 910 920 930 940 950 960 VFSPGRKNGS FIIDGKSRKE CPFSNRVWNS FQIEEFGTGV FTTRVYMDAV FEYTIDCDGS 970 980 990 1000 1010 1020 ILGAAVNGKK SAHGSPTFWM GSHEVNGTWM IHTLEALDYK ECEWPLTHTI GTSVEESEMF 1030 1040 1050 1060 1070 1080 MPRSIGGPVS SHNHIPGYKV QTNGPWMQVP LEVKREACPG TSVIIDGNCD GRGKSTRSTT 1090 1100 1110 1120 1130 1140 DSGKVIPEWC CRSCTMPPVS FHGSDGCWYP MEIRPRKTHE SHLVRSWVTA GEIHAVPFGL 1150 1160 1170 1180 1190 1200 VSMMIAMEVV LRKRQGPKQM LVGGVVLLGA MLVGQVTLLD LLKLTVAVGL HFHEMNNGGD 1210 1220 1230 1240 1250 1260 AMYMALIAAF SIRPGLLIGF GLRTLWSPRE RLVLTLGAAM VEIALGGVMG GLWKYLNAVS 1270 1280 1290 1300 1310 1320 LCILTINAVA SRKASNTILP LMALLTPVTM AEVRLAAMFF CAVVIIGVLH QNFKDTSMQK 1330 1340 1350 1360 1370 1380 TIPLVALTLT SYLGLTQPFL GLCAFLATRI FGRRSIPVNE ALAAAGLVGV LAGLAFQEME 1390 1400 1410 1420 1430 1440 NFLGPIAVGG LLMMLVSVAG RVDGLELKKL GEVSWEEEAE ISGSSARYDV ALSEQGEFKL 1450 1460 1470 1480 1490 1500 LSEEKVPWDQ VVMTSLALVG AALHPFALLL VLAGWLFHVR GARRSGDVLW DIPTPKIIEE 1510 1520 1530 1540 1550 1560 CEHLEDGIYG IFQSTFLGAS QRGVGVAQGG VFHTMWHVTR GAFLVRNGKK LIPSWASVKE 1570 1580 1590 1600 1610 1620 DLVAYGGSWK LEGRWDGEEE VQLIAAVPGK NVVNVQTKPS LFKVRNGGEI GAVALDYPSG 1630 1640 1650 1660 1670 1680 TSGSPIVNRN GEVIGLYGNG ILVGDNSFVS AISQTEVKEE GKEELQEIPT MLKKGMTTVL 1690 1700 1710 1720 1730 1740 DFHPGAGKTR RFLPQILAEC ARRRLRTLVL APTRVVLSEM KEAFHGLDVK FHTQAFSAHG 1750 1760 1770 1780 1790 1800 SGREVIDAMC HATLTYRMLE PTRVVNWEVI IMDEAHFLDP ASIAARGWAA HRARANESAT 1810 1820 1830 1840 1850 1860 ILMTATPPGT SDEFPHSNGE IEDVQTDIPS EPWNTGHDWI LADKRPTAWF LPSIRAANVM 1870 1880 1890 1900 1910 1920 AASLRKAGKS VVVLNRKTFE REYPTIKQKK PDFILATDIA EMGANLCVER VLDCRTAFKP 1930 1940 1950 1960 1970 1980 VLVDEGRKVA IKGPLRISAS SAAQRRGRIG RNPNRDGDSY YYSEPTSENN AHHVCWLEAS 1990 2000 2010 2020 2030 2040 MLLDNMEVRG GMVAPLYGVE GTKTPVSPGE MRLRDDQRKV FRELVRNCDL PVWLSWQVAK 2050 2060 2070 2080 2090 2100 AGLKTNDRKW CFEGPEEHEI LNDSGETVKC RAPGGAKKPL RPRWCDERVS SDQSALSEFI 2110 2120 2130 2140 2150 2160 KFAEGRRGAA EVLVVLSELP DFLAKKGGEA MDTISVFLHS EEGSRAYRNA LSMMPEAMTI 2170 2180 2190 2200 2210 2220 VMLFILAGLL TSGMVIFFMS PKGISRMSMA MGTMAGCGYL MFLGGVKPTH ISYVMLIFFV 2230 2240 2250 2260 2270 2280 LMVVVIPEPG QQRSIQDNQV AYLIIGILTL VSAVAANELG MLEKTKEDLF GKKNLIPSSA 2290 2300 2310 2320 2330 2340 SPWSWPDLDL KPGAAWTVYV GIVTMLSPML HHWIKVEYGN LSLSGIAQSA SVLSFMDKGI 2350 2360 2370 2380 2390 2400 PFMKMNISVI MLLVSGWNSI TVMPLLCGIG CAMLHWSLIL PGIKAQQSKL AQRRVFHGVA 2410 2420 2430 2440 2450 2460 ENPVVDGNPT VDIEEAPEMP ALYEKKLALY LLLALSLASV AMCRTPFSLA EGIVLASAAL 2470 2480 2490 2500 2510 2520 GPLIEGNTSL LWNGPMAVSM TGVMRGNHYA FVGVMYNLWK MKTGRRGSAN GKTLGEVWKR 2530 2540 2550 2560 2570 2580 ELNLLDKRQF ELYKRTDIVE VDRDTARRHL AEGKVDTGVA VSRGTAKLRW FHERGYVKLE 2590 2600 2610 2620 2630 2640 GRVIDLGCGR GGWCYYAAAQ KEVSGVKGFT LGRDGHEKPM NVQSLGWNII TFKDKTDIHR 2650 2660 2670 2680 2690 2700 LEPVKCDTLL CDIGESSSSS VTEGERTVRV LDTVEKWLAC GVDNFCVKVL APYMPDVLEK 2710 2720 2730 2740 2750 2760 LELLQRRFGG TVIRNPLSRN STHEMYYVSG ARSNVTFTVN QTSRLLMRRM RRPTGKVTLE 2770 2780 2790 2800 2810 2820 ADVILPIGTR SVETDKGPLD KEAIEERVER IKSEYMTSWF YDNDNPYRTW HYCGSYVTKT 2830 2840 2850 2860 2870 2880 SGSAASMVNG VIKILTYPWD RIEEVTRMAM TDTTPFGQQR VFKEKVDTRA KDPPAGTRKI 2890 2900 2910 2920 2930 2940 MKVVNRWLFR HLAREKNPRL CTKEEFIAKV RSHAAIGAYL EEQEQWKTAN EAVQDPKFWE 2950 2960 2970 2980 2990 3000 LVDEERKLHQ QGRCRTCVYN MMGKREKKLS EFGKAKGSRA IWYMWLGARY LEFEALGFLN 3010 3020 3030 3040 3050 3060 EDHWASRENS GGGVEGIGLQ YLGYVIRDLA AMDGGGFYAD DTAGWDTRIT EADLDDEQEI 3070 3080 3090 3100 3110 3120 LNYMSPHHKK LAQAVMEMTY KNKVVKVLRP APGGKAYMDV ISRRDQRGSG QVVTYALNTI 3130 3140 3150 3160 3170 3180 TNLKVQLIRM AEAEMVIHHQ HVQDCDESVL TRLEAWLTEH GCDRLKRMAV SGDDCVVRPI 3190 3200 3210 3220 3230 3240 DDRFGLALSH LNAMSKVRKD ISEWQPSKGW NDWENVPFCS HHFHELQLKD GRRIVVPCRE 3250 3260 3270 3280 3290 3300 QDELIGRGRV SPGNGWMIKE TACLSKAYAN MWSLMYFHKR DMRLLSLAVS SAVPTSWVPQ 3310 3320 3330 3340 3350 3360 GRTTWSIHGK GEWMTTEDML EVWNRVWITN NPHMQDKTMV KKWRDVPYLT KRQDKLCGSL 3370 3380 3390 3400 3410 IGMTNRATWA SHIHLVIHRI RTLIGQEKYT DYLTVMDRYS VDADLQLGEL I

References

[1]	"Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution." Rice C.M., Lenches E.M., Eddy S.R., Shin S.J., Sheets R.L., Strauss J.H. Science 229:726-733(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Complete nucleotide sequence of yellow fever virus vaccine strains 17DD and 17D-213." dos Santos C.N., Post P.R., Carvalho R., Ferreira I.I., Rice C.M., Galler R. Virus Res. 35:35-41(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate 17D-213 vaccine and Isolate 17DD vaccine.
[3]	"Yellow fever 17D vaccine virus isolated from healthy vaccinees accumulates very few mutations." Xie H., Cass A.R., Barrett A.D.T. Virus Res. 55:93-99(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate 17D-204-USA HONG1 vaccine, Isolate 17D-204-USA HONG2 vaccine and Isolate 17D-204-USA HONG3 vaccine.
[4]	"Nucleotide sequence comparison of the genome of two 17D-204 yellow fever vaccines." Dupuy A., Despres P., Cahour A., Girard M., Bouloy M. Nucleic Acids Res. 17:3989-3989(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Pasteur 17D-204 vaccine.
[5]	"Mutation in NS5 protein attenuates mouse neurovirulence of yellow fever 17D vaccine virus." Xie H., Ryman K.D., Campbell G.A., Barrett A.D.T. J. Gen. Virol. 79:1895-1899(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate 17D-204-South Africa vaccine, Isolate 17D-204-South Africa vaccine large plaque variant and Isolate 17D-204-South Africa vaccine medium plaque variant.
[6]	"Yellow fever vaccine-associated viscerotropic disease and death in Spain." Doblas A., Domingo C., Bae H.G., Bohorquez C.L., de Ory F., Niedrig M., Mora D., Carrasco F.J., Tenorio A. J. Clin. Virol. 36:156-158(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Spain/AVD2791-93F/2004 vaccine.
[7]	"Characterization of a viscerotropic yellow fever vaccine variant from a patient in Brazil." Engel A.R., Vasconcelos P.F., McArthur M.A., Barrett A.D. Vaccine 24:2803-2809(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Isolate Brazil/YF-VAVD/1975 vaccine.
[8]	"Partial N-terminal amino acid sequences of three nonstructural proteins of two flaviviruses." Rice C.M., Aebersold R., Teplow D.B., Pata J., Bell J.R., Vorndam A.V., Trent D.W., Brandriss M.W., Schlesinger J.J., Strauss J.H. Virology 151:1-9(1986) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 779-798; 1485-1497 AND 2507-2510.
[9]	"Yellow fever virus proteins NS2A, NS2B, and NS4B: identification and partial N-terminal amino acid sequence analysis." Chambers T.J., McCourt D.W., Rice C.M. Virology 169:100-109(1989) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2257-2276.
[10]	"Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine protease responsible for site-specific cleavages in the viral polyprotein." Chambers T.J., Weir R.C., Grakoui A., McCourt D.W., Bazan J.F., Fletterick R.J., Rice C.M. Proc. Natl. Acad. Sci. U.S.A. 87:8898-8902(1990) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION OF NS2B-NS3 PROTEASE, MUTAGENESIS OF HIS-1537; ASP-1561 AND SER-1622.
[11]	"Mutagenesis of the yellow fever virus NS2B/3 cleavage site: determinants of cleavage site specificity and effects on polyprotein processing and viral replication." Chambers T.J., Nestorowicz A., Rice C.M. J. Virol. 69:1600-1605(1995) [PubMed] [Europe PMC] [Abstract] Cited for: CHARACTERIZATION OF NS2B-NS3 PROTEASE.
[12]	"Mutagenesis of conserved residues at the yellow fever virus 3/4A and 4B/5 dibasic cleavage sites: effects on cleavage efficiency and polyprotein processing." Lin C., Chambers T.J., Rice C.M. Virology 192:596-604(1993) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ARG-2107; ARG-2505 AND ARG-2506.
[13]	"Cleavage at a novel site in the NS4A region by the yellow fever virus NS2B-3 proteinase is a prerequisite for processing at the downstream 4A/4B signalase site." Lin C., Amberg S.M., Chambers T.J., Rice C.M. J. Virol. 67:2327-2335(1993) [PubMed] [Europe PMC] [Abstract] Cited for: CLEAVAGE OF NS4A/NS4B.
[14]	"NS2B-3 proteinase-mediated processing in the yellow fever virus structural region: in vitro and in vivo studies." Amberg S.M., Nestorowicz A., McCourt D.W., Rice C.M. J. Virol. 68:3794-3802(1994) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF NS2B-NS3 PROTEASE.
[15]	"Mutagenesis of the yellow fever virus NS2A/2B cleavage site: effects on proteolytic processing, viral replication, and evidence for alternative processing of the NS2A protein." Nestorowicz A., Chambers T.J., Rice C.M. Virology 199:114-123(1994) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF PHE-1351; GLY-1352; ARG-1353; ARG-1354 AND SER-1355.
[16]	"Mutagenesis of the N-linked glycosylation sites of the yellow fever virus NS1 protein: effects on virus replication and mouse neurovirulence." Muylaert I.R., Chambers T.J., Galler R., Rice C.M. Virology 222:159-168(1996) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASN-908; SER-910; ASN-986 AND THR-988.
[17]	"Genetic analysis of the yellow fever virus NS1 protein: identification of a temperature-sensitive mutation which blocks RNA accumulation." Muylaert I.R., Galler R., Rice C.M. J. Virol. 71:291-298(1997) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ARG-1077.
[18]	"trans-Complementation of yellow fever virus NS1 reveals a role in early RNA replication." Lindenbach B.D., Rice C.M. J. Virol. 71:9608-9617(1997) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF NS1.
[19]	"The NS5A/NS5 proteins of viruses from three genera of the family flaviviridae are phosphorylated by associated serine/threonine kinases." Reed K.E., Gorbalenya A.E., Rice C.M. J. Virol. 72:6199-6206(1998) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION OF RNA-DIRECTED RNA POLYMERASE NS5.
[20]	"Genetic interaction of flavivirus nonstructural proteins NS1 and NS4A as a determinant of replicase function." Lindenbach B.D., Rice C.M. J. Virol. 73:4611-4621(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION OF NS1 WITH NS4A.
[21]	"Mutagenesis of the NS2B-NS3-mediated cleavage site in the flavivirus capsid protein demonstrates a requirement for coordinated processing." Amberg S.M., Rice C.M. J. Virol. 73:8083-8094(1999) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF 99-ARG--ARG-101.
[22]	"Mutagenesis of the signal sequence of yellow fever virus prM protein: enhancement of signalase cleavage In vitro is lethal for virus production." Lee E., Stocks C.E., Amberg S.M., Rice C.M., Lobigs M. J. Virol. 74:24-32(2000) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF 116-LEU--GLY-121.
[23]	"Yellow fever virus NS2B-NS3 protease: charged-to-alanine mutagenesis and deletion analysis define regions important for protease complex formation and function." Droll D.A., Krishna Murthy H.M., Chambers T.J. Virology 275:335-347(2000) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF 1406-GLU--LYS-1409.
[24]	"Mutations in the yellow fever virus nonstructural protein NS2A selectively block production of infectious particles." Kummerer B.M., Rice C.M. J. Virol. 76:4773-4784(2002) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF GLN-1319; LYS-1320 AND THR-1321.
[25]	"Flavivirus capsid is a dimeric alpha-helical protein." Jones C.T., Ma L., Burgner J.W., Groesch T.D., Post C.B., Kuhn R.J. J. Virol. 77:7143-7149(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT.
[26]	"The transmembrane domains of the prM and E proteins of yellow fever virus are endoplasmic reticulum localization signals." Op De Beeck A., Rouille Y., Caron M., Duvet S., Dubuisson J. J. Virol. 78:12591-12602(2004) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION OF SMALL ENVELOPE PROTEIN M AND ENVELOPE PROTEIN E.
[27]	"Inhibition of alpha/beta interferon signaling by the NS4B protein of flaviviruses." Munoz-Jordan J.L., Laurent-Rolle M., Ashour J., Martinez-Sobrido L., Ashok M., Lipkin W.I., Garcia-Sastre A. J. Virol. 79:8004-8013(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF NON-STRUCTURAL PROTEIN 4B.
[28]	"Structure and function of flavivirus NS5 methyltransferase." Zhou Y., Ray D., Zhao Y., Dong H., Ren S., Li Z., Guo Y., Bernard K.A., Shi P.-Y., Li H. J. Virol. 81:3891-3903(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF RNA-DIRECTED RNA POLYMERASE NS5.
[29]	"The flavivirus NS5 protein is a true RNA guanylyltransferase that catalyzes a two-step reaction to form the RNA cap structure." Issur M., Geiss B.J., Bougie I., Picard-Jean F., Despins S., Mayette J., Hobdey S.E., Bisaillon M. RNA 15:2340-2350(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF RNA-DIRECTED RNA POLYMERASE NS5.
[30]	"Structures of immature flavivirus particles." Zhang Y., Corver J., Chipman P.R., Zhang W., Pletnev S.V., Sedlak D., Baker T.S., Strauss J.H., Kuhn R.J., Rossmann M.G. EMBO J. 22:2604-2613(2003) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY ELECTRON MICROSCOPY (25 ANGSTROMS) OF IMMATURE PARTICLES.
[31]	"Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing." Wu J., Bera A.K., Kuhn R.J., Smith J.L. J. Virol. 79:10268-10277(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1671-2107.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X03700 Genomic RNA. Translation: CAA27332.1.
X15062 Genomic RNA. Translation: CAB37419.1.
U17066 Genomic RNA. Translation: AAC54267.1.
U17067 Genomic RNA. Translation: AAC54268.1.
AF052437 Genomic RNA. Translation: AAC35899.1.
AF052438 Genomic RNA. Translation: AAC35900.1.
AF052439 Genomic RNA. Translation: AAC35901.1.
AF052444 Genomic RNA. Translation: AAC35906.1.
AF052445 Genomic RNA. Translation: AAC35907.1.
AF052446 Genomic RNA. Translation: AAC35908.1.
DQ118157 Genomic RNA. Translation: AAZ31436.1.
DQ100292 Genomic RNA. Translation: AAZ07885.1.

PIR

GNWVY. A03914.
GNWVYP. S07757.

RefSeq

NP_041726.1. NC_002031.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1NA4	electron microscopy	-
1YKS	X-ray	1.80	A	1671-2107	[»]
1YMF	X-ray	2.60	A	1671-2107	[»]
3EVA	X-ray	1.50	A	2507-2772	[»]
3EVB	X-ray	1.85	A	2507-2772	[»]
3EVC	X-ray	1.60	A	2507-2772	[»]
3EVD	X-ray	1.50	A	2507-2772	[»]
3EVE	X-ray	1.70	A	2507-2772	[»]
3EVF	X-ray	1.45	A	2507-2772	[»]

ProteinModelPortal

P03314.

SMR

P03314. Positions 572-683, 1490-1667, 1671-2107, 2512-2772, 2780-3399.

ModBase

Search...

Proteomic databases

PRIDE

P03314.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

2.60.40.350. 1 hit.
2.60.98.10. 2 hits.
3.30.387.10. 1 hit.

InterPro

IPR011492. DEAD_Flavivir.
IPR000069. Env_glycoprot_M_flavivir.
IPR013755. Flav_gly_cen_dom_subdom1.
IPR001122. Flavi_capsidC.
IPR026470. Flavi_E_Stem/Anchor_dom.
IPR001157. Flavi_NS1.
IPR000752. Flavi_NS2A.
IPR000487. Flavi_NS2B.
IPR000404. Flavi_NS4A.
IPR001528. Flavi_NS4B.
IPR002535. Flavi_propep.
IPR000336. Flavivir/Alphavir_Ig-like.
IPR001850. Flavivirus_NS3_S7.
IPR027287. Flavovir_Ig-like.
IPR014412. Gen_Poly_FLV.
IPR011998. Glycoprot_cen/dimer.
IPR013754. GlyE_dim.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR014756. Ig_E-set.
IPR026490. mRNA_cap_0/1_MeTrfase.
IPR000208. RNA-dir_pol_flavivirus.
IPR007094. RNA-dir_pol_PSvirus.
IPR002877. rRNA_MeTrfase_FtsJ_dom.
IPR009003. Trypsin-like_Pept_dom.
[Graphical view]

Pfam

PF01003. Flavi_capsid. 1 hit.
PF07652. Flavi_DEAD. 1 hit.
PF02832. Flavi_glycop_C. 1 hit.
PF00869. Flavi_glycoprot. 1 hit.
PF01004. Flavi_M. 1 hit.
PF00948. Flavi_NS1. 1 hit.
PF01005. Flavi_NS2A. 1 hit.
PF01002. Flavi_NS2B. 1 hit.
PF01350. Flavi_NS4A. 1 hit.
PF01349. Flavi_NS4B. 1 hit.
PF00972. Flavi_NS5. 1 hit.
PF01570. Flavi_propep. 1 hit.
PF01728. FtsJ. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00949. Peptidase_S7. 1 hit.
[Graphical view]

PIRSF

PIRSF003817. Gen_Poly_FLV. 1 hit.

SMART

SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]

SUPFAM

SSF56983. Flavi_glycoprotE. 1 hit.
SSF81296. Ig_E-set. 1 hit.
SSF50494. Pept_Ser_Cys. 1 hit.

TIGRFAMs

TIGR04240. flavi_E_stem. 1 hit.

PROSITE

PS51527. FLAVIVIRUS_NS2B. 1 hit.
PS51528. FLAVIVIRUS_NS3PRO. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. False negative.
PS50507. RDRP_SSRNA_POS. 1 hit.
PS51591. RNA_CAP01_NS5_MT. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P03314.

Entry information

Entry name

POLG_YEFV1

Accession

Primary (citable) accession number: P03314
Secondary accession number(s): O42028 , O91857, P19901, Q102J3, Q45RQ2, Q89275, Q89276, Q9W878, Q9YWN0, Q9YWN1, Q9YWN2

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	May 1, 2013
This is version 141 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program