P03495 (NS1_I72A2) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Non-structural protein 1
Short name=NS1

Alternative name(s):
NS1A

Gene names

Name:

NS

Organism

Influenza A virus (strain A/Udorn/307/1972 H3N2) [Complete proteome]

Taxonomic identifier

381517 [NCBI]

Taxonomic lineage

Viruses › ssRNA viruses › ssRNA negative-strand viruses › Orthomyxoviridae › Influenzavirus A › Influenza A virus › H3N2 subtype

Virus host

Aves [TaxID: 8782]
Cetacea (whales) [TaxID: 9721]
Homo sapiens (Human) [TaxID: 9606]
Phocidae (true seals) [TaxID: 9709]
Sus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length	237 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Inhibits post-transcriptional processing of cellular pre-mRNA, by binding and inhibiting two cellular proteins that are required for the 3'-end processing of cellular pre-mRNAs: the 30 kDa cleavage and polyadenylation specificity factor (CPSF4) and the poly(A)-binding protein 2 (PABPN1). This results in the accumulation of unprocessed 3' end pre-mRNAs which can't be exported from the nucleus. Cellular protein synthesis is thereby shut off very early after virus infection. Viral protein synthesis is not affected by the inhibition of the cellular 3' end processing machinery because the poly(A) tails of viral mRNAs are produced by the viral polymerase through a stuttering mechanism. Ref.6 Ref.8 Ref.12 Prevents the establishment of the cellular antiviral state by inhibiting TRIM25-mediated DDX58 ubiquitination, which normally triggers the antiviral transduction signal that leads to the activation of type I IFN genes by transcription factors like IRF3 and IRF7. Prevents human EIF2AK2/PKR activation, either by binding double-strand RNA, or by interacting directly with EIF2AK2/PKR. This function may be important at the very beginning of the infection, when NS1 is mainly present in the cytoplasm. Also binds poly(A) and U6 snRNA. Suppresses the RNA silencing-based antiviral response in Drosophila cells By similarity. Ref.6 Ref.8 Ref.12
Subunit structure	Homodimer. Interacts with host TRIM25 (via coiled coil); this interaction specifically inhibits TRIM25 multimerization and TRIM25-mediated DDX58 CARD ubiquitination By similarity. Interacts with human EIF2AK2/PKR, CPSF4, IVNS1ABP and PABPN1. Ref.4 Ref.6 Ref.7 Ref.9 Ref.12
Subcellular location	Host nucleus. Host cytoplasm. Note: In uninfected, transfected cells, NS1 is localized in the nucleus. Only in virus infected cells, the nuclear export signal is unveiled, presumably by a viral protein, and a fraction of NS1 is exported in the cytoplasm.
Domain	The dsRNA-binding region is required for suppression of RNA silencing By similarity.
Sequence similarities	Belongs to the influenza A viruses NS1 family.

Ontologies

Keywords
Biological process	Host gene expression shutoff by virus Host mRNA suppression by virus Host-virus interaction Inhibition of host IFN-mediated response initiation by virus Inhibition of host PKR by virus Inhibition of host RIG-I by virus Inhibition of host innate immune response by virus Inhibition of host interferon signaling pathway by virus Inhibition of host pre-mRNA processing by virus Interferon antiviral system evasion Viral immunoevasion
Cellular component	Host cytoplasm Host nucleus
Coding sequence diversity	Alternative splicing
Ligand	RNA-binding
Molecular function	Suppressor of RNA silencing
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	modulation by symbiont of host intracellular transport Inferred from direct assay PubMed 17079289. Source: BHF-UCL modulation by virus of host transcription Inferred from direct assay PubMed 17079289. Source: BHF-UCL negative regulation by symbiont of host innate immune response Inferred from direct assay PubMed 17079289. Source: BHF-UCL suppression by virus of host PKR activity Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host RIG-I activity Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host cytokine production Inferred from direct assay PubMed 17079289. Source: BHF-UCL suppression by virus of host mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW suppression by virus of host type I interferon production 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
Cellular_component	host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	double-stranded RNA binding Traceable author statement PubMed 17079289. Source: BHF-UCL
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform NS1 (identifier: P03495-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform NEP (identifier: P69258-1)

Also known as: NS2;

The sequence of this isoform can be found in the external entry P69258.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 237

237

Non-structural protein 1

PRO_0000078952

Regions

Region

1 – 73

73

RNA-binding and homodimerization

Region

180 – 215

36

CPSF4-binding

Region

223 – 237

15

PABPN1-binding

Motif

34 – 38

5

Nuclear localization signal 1

Motif

137 – 146

10

Nuclear export signal

Motif

216 – 221

6

Nuclear localization signal 2

Experimental info

Mutagenesis

7 – 8

2

SS → AA: No effect on nuclear mRNA export inhibition.

Mutagenesis

7 – 8

2

SS → DL: Complete loss of nuclear mRNA export inhibition.

Mutagenesis

19 – 20

2

RK → AA or DL: Complete loss of nuclear mRNA export inhibition.

Mutagenesis

31 – 32

2

PF → AA: Complete loss of nuclear mRNA export inhibition.

Mutagenesis

35 – 38

4

RLRR → ALAA: 75% loss of nuclear mRNA export inhibition. Ref.3

Mutagenesis

39 – 40

2

DQ → AA: No effect on nuclear mRNA export inhibition.

Mutagenesis

48 – 49

2

ST → DL: No effect on nuclear mRNA export inhibition.

Mutagenesis

62 – 63

2

KQ → AA: No effect on nuclear mRNA export inhibition.

Mutagenesis

62 – 63

2

KQ → DL: Complete loss of nuclear mRNA export inhibition.

Mutagenesis

73 – 74

2

SD → DL: No effect on nuclear mRNA export inhibition.

Mutagenesis

87 – 88

2

SR → DL: No effect on nuclear mRNA export inhibition.

Mutagenesis

99 – 100

2

SR → DL: No effect on nuclear mRNA export inhibition.

Mutagenesis

116 – 117

2

CI → DL: No effect on nuclear mRNA export inhibition.

Mutagenesis

134 – 136

3

FSV → AAA or LDL: Complete loss of nuclear mRNA export inhibition. Ref.3

Mutagenesis

141

1

L → A: No effect on nuclear mRNA export inhibition. Ref.3

Mutagenesis

144

1

L → A: Complete loss of nuclear mRNA export inhibition. Ref.3

Mutagenesis

146

1

L → A: Complete loss of nuclear mRNA export inhibition. Ref.3

Mutagenesis

150 – 151

2

FT → AA or DL: Complete loss of nuclear mRNA export inhibition.

Mutagenesis

160 – 161

2

IS → AA or DL: Complete loss of nuclear mRNA export inhibition.

Mutagenesis

175 – 176

2

KN → AA: No effect on nuclear mRNA export inhibition.

Mutagenesis

186 – 187

2

EW → AS: Complete loss of CPSF4 binding.

Mutagenesis

199 – 200

2

QR → AA: No effect on nuclear mRNA export inhibition.

Mutagenesis

201 – 203

3

FAW → AAA: No effect on CPSF4 binding. Ref.10

Mutagenesis

205 – 206

2

SS → AA: No effect on nuclear mRNA export inhibition.

Mutagenesis

212 – 213

2

PP → AA: No effect on CPSF4 binding.

Mutagenesis

219 – 221

3

KRK → ARA: No effect on nuclear mRNA export inhibition.

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

237

Helix Strand Turn

Details...

Helix

3 – 24

22

Helix

30 – 50

21

Helix

54 – 69

16

Beta strand

88 – 91

4

Helix

95 – 99

5

Beta strand

105 – 112

8

Beta strand

115 – 120

6

Beta strand

127 – 137

11

Beta strand

140 – 151

12

Beta strand

156 – 162

7

Beta strand

164 – 166

3

Helix

171 – 187

17

Beta strand

191 – 194

4

Helix

196 – 201

6

Turn

202 – 205

4

Sequences

	Sequence		Length	Mass (Da)
	Isoform NS1 [UniParc]. Last modified July 21, 1986. Version 1. Checksum: 14D0308795627E5E	FASTA	237	26,846
	10 20 30 40 50 60 MDSNTVSSFQ VDCFLWHVRK QVVDQELGDA PFLDRLRRDQ KSLRGRGSTL GLNIEAATHV 70 80 90 100 110 120 GKQIVEKILK EESDEALKMT MASTPASRYI TDMTIEELSR DWFMLMPKQK VEGPLCIRID 130 140 150 160 170 180 QAIMDKNIML KANFSVIFDR LETLILLRAF TEEGAIVGEI SPLPSFPGHT IEDVKNAIGV 190 200 210 220 230 LIGGLEWNDN TVRVSKTLQR FAWGSSNENG RPPLTPKQKR KMARTARSKV RRDKMAD
	Isoform NEP (NS2) [UniParc]. See P69258.		–	–

References

[1]	"Sequence of interrupted and uninterrupted mRNAs and cloned DNA coding for the two overlapping nonstructural proteins of influenza virus." Lamb R.A., Lai C.-J. Cell 21:475-485(1980) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Complete genome sequencing and analysis of selected influenza virus vaccine strains spanning six decades (1933-1999)." Mbawuike I.N., Zhang Y., Yamada R.E., Nino D., Bui H.-H., Sette A., Couch R.B. Submitted (APR-2006) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[3]	"Two functional domains of the influenza virus NS1 protein are required for regulation of nuclear export of mRNA." Qian X.Y., Alonso-Caplen F., Krug R.M. J. Virol. 68:2433-2441(1994) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF 7-SER-SER-8; 19-ARG-PHE-20; 31-PRO-PHE-32; 35-ARG--ARG-38; 39-ASP-GLN-40; 48-SER-THR-49; 62-LYS-GLN-63; 73-SER-ASP-74; 87-SER-ARG-88; 99-SER-ARG-100; 116-CYS-ILE-117; 134-PHE--VAL-136; LEU-141; LEU-144; LEU-146; 150-PHE-THR-151; 160-ILE-SER-161; 175-LYS-ASN-176; 199-GLN-ARG-200; 205-SER-SER-206 AND 219-LYS-LYS-221.
[4]	"The influenza virus NS1 protein forms multimers in vitro and in vivo." Nemeroff M.E., Qian X.Y., Krug R.M. Virology 212:422-428(1995) [PubMed] [Europe PMC] [Abstract] Cited for: DIMERIZATION.
[5]	"The RNA-binding and effector domains of the viral NS1 protein are conserved to different extents among influenza A and B viruses." Wang W., Krug R.M. Virology 223:41-50(1996) [PubMed] [Europe PMC] [Abstract] Cited for: RNA-BINDING.
[6]	"Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 3'end formation of cellular pre-mRNAs." Nemeroff M.E., Barabino S.M.L., Li Y., Keller W., Krug R.M. Mol. Cell 1:991-1000(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH HUMAN CPSF4.
[7]	"Biochemical and genetic evidence for complex formation between the influenza A virus NS1 protein and the interferon-induced PKR protein kinase." Tan S.L., Katze M.G. J. Interferon Cytokine Res. 18:757-766(1998) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HUMAN EIF2AK2/PKR.
[8]	"Regulation of a nuclear export signal by an adjacent inhibitory sequence: the effector domain of the influenza virus NS1 protein." Li Y., Yamakita Y., Krug R.M. Proc. Natl. Acad. Sci. U.S.A. 95:4864-4869(1998) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[9]	"Influenza A virus NS1 protein targets poly(A)-binding protein II of the cellular 3'-end processing machinery." Chen Z., Li Y., Krug R.M. EMBO J. 18:2273-2283(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HUMAN PABPN1.
[10]	"The 3'-end-processing factor CPSF is required for the splicing of single-intron pre-mRNAs in vivo." Li Y., Chen Z.Y., Wang W., Baker C.C., Krug R.M. RNA 7:920-931(2001) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF 186-GLU-TRP-187; 201-PHE--TRP-203 AND 212-PRO-PRO-213.
[11]	"Intracellular warfare between human influenza viruses and human cells: the roles of the viral NS1 protein." Krug R.M., Yuan W., Noah D.L., Latham A.G. Virology 309:181-189(2003) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[12]	"The CPSF30 binding site on the NS1A protein of influenza A virus is a potential antiviral target." Twu K.Y., Noah D.L., Rao P., Kuo R.L., Krug R.M. J. Virol. 80:3957-3965(2006) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH HOST CPSF4.
[13]	"A novel RNA-binding motif in influenza A virus non-structural protein 1." Chien C.Y., Tejero R., Huang Y., Zimmerman D.E., Rios C.B., Krug R.M., Montelione G.T. Nat. Struct. Biol. 4:891-895(1997) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 1-73.
[14]	"Crystal structure of the unique RNA-binding domain of the influenza virus NS1 protein." Liu J., Lynch P.A., Chien C.Y., Montelione G.T., Krug R.M., Berman H.M. Nat. Struct. Biol. 4:896-899(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-72.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

V01102 Genomic RNA. Translation: CAA24288.1.
DQ508933 Genomic RNA. Translation: ABF21224.1.

PIR

MNIV1A. A04088.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AIL	X-ray	1.90	A	1-72	[»]
1NS1	NMR	-	A/B	1-73	[»]
2KKZ	NMR	-	A	85-215	[»]
2RHK	X-ray	1.95	A/B	85-215	[»]
3EE8	X-ray	2.60	A/B	84-205	[»]
3EE9	X-ray	2.14	A/B	84-205	[»]
3KWG	X-ray	2.21	A/B	78-205	[»]
3KWI	X-ray	2.21	A/B	78-205	[»]

ProteinModelPortal

P03495.

SMR

P03495. Positions 1-73, 85-203.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-46282N.

IntAct

P03495. 44 interactions.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

1.10.287.10. 1 hit.

InterPro

IPR000256. Flu_NS1.
IPR009068. S15_NS1_RNA-bd.
[Graphical view]

Pfam

PF00600. Flu_NS1. 1 hit.
[Graphical view]

SUPFAM

SSF47060. S15/NS1_bind. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P03495.

Entry information

Entry name

NS1_I72A2

Accession

Primary (citable) accession number: P03495
Secondary accession number(s): Q1K9D5

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	July 21, 1986
Last modified:	April 3, 2013
This is version 97 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program