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Protein

Structural polyprotein

Gene
N/A
Organism
Semliki forest virus (SFV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Capsid protein: Possesses a protease activity that results in its autocatalytic cleavage from the nascent structural protein. Following its self-cleavage, the capsid protein transiently associates with ribosomes, and within several minutes the protein binds to viral RNA and rapidly assembles into icosaedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of E2 at the cell membrane, leading to budding and formation of mature virions. New virions attach to target cells, and after clathrin-mediated endocytosis their membrane fuses with the host endosomal membrane. This leads to the release of the nucleocapsid into the cytoplasm, followed by an uncoating event necessary for the genomic RNA to become accessible. The uncoating might be triggered by the interaction of capsid proteins with ribosomes. Binding of ribosomes would release the genomic RNA since the same region is genomic RNA-binding and ribosome-binding.2 Publications
Protein E3: Provides the signal sequence for p62 (E3/E2) translocation to the host endoplasmic reticulum. Mediates pH protection of E1 during secretory pathway trans- port.1 Publication
Envelope glycoprotein E2: Plays a role in viral attachment to target host cell, by binding to the cell receptor. Synthesized as a p62 precursor which is processed by furin at the cell membrane just before virion budding, giving rise to E2-E1 heterodimer. The p62-E1 heterodimer is stable, whereas E2-E1 is unstable and dissociate at low pH. p62 is processed at the last step, presumably to avoid E1 fusion activation before its final export to cell surface. E2 C-terminus contains a transitory transmembrane that would be disrupted by palmitoylation, resulting in reorientation of the C-terminal tail from lumenal to cytoplasmic side. This step is critical since E2 C-terminus is involved in budding by interacting with capsid proteins. This release of E2 C-terminus in cytoplasm occurs lately in protein export, and precludes premature assembly of particles at the endoplasmic reticulum membrane.1 Publication
Protein 6K: Constitutive membrane protein involved in virus glycoprotein processing, cell permeabilization, and the budding of viral particles. Disrupts the calcium homeostasis of the cell, probably at the endoplasmic reticulum level. This leads to cytoplasmic calcium elevation. Because of its lipophilic properties, the 6K protein is postulated to influence the selection of lipids that interact with the transmembrane domains of the glycoproteins, which, in turn, affects the deformability of the bilayer required for the extreme curvature that occurs as budding proceeds. Present in low amount in virions, about 3% compared to viral glycoproteins.2 Publications
Envelope glycoprotein E1: Class II viral fusion protein. Fusion activity is inactive as long as E1 is bound to E2 in mature virion. After virus attachment to target cell and endocytosis, acidification of the endosome would induce dissociation of E1/E2 heterodimer and concomitant trimerization of the E1 subunits. This E1 trimer is fusion active, and promotes release of viral nucleocapsid in cytoplasm after endosome and viral membrane fusion. Efficient fusion requires the presence of cholesterol and sphingolipid in the target membrane. Fusion is optimal at levels of about 1 molecule of cholesterol per 2 molecules of phospholipids, and is specific for sterols containing a 3-beta-hydroxyl group.1 Publication

Catalytic activityi

Autocatalytic release of the core protein from the N-terminus of the togavirus structural polyprotein by hydrolysis of a -Trp-|-Ser- bond.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei145 – 1451Charge relay systemPROSITE-ProRule annotation
Active sitei151 – 1511Charge relay systemPROSITE-ProRule annotation
Active sitei219 – 2191Charge relay systemPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine protease

Keywords - Biological processi

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, Viral attachment to host cell, Viral penetration into host cytoplasm, Virus endocytosis by host, Virus entry into host cell

Protein family/group databases

MEROPSiS03.001.
TCDBi1.G.4.1.1. the viral pore-forming membrane fusion protein-4 (vmfp4) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Structural polyprotein
Alternative name(s):
p130
Cleaved into the following 6 chains:
Alternative name(s):
Coat protein
Short name:
C
Alternative name(s):
E3/E2
Alternative name(s):
Spike glycoprotein E3
Alternative name(s):
Spike glycoprotein E2
Alternative name(s):
Spike glycoprotein E1
OrganismiSemliki forest virus (SFV)
Taxonomic identifieri11033 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageTogaviridaeAlphavirusSFV complex
Virus hostiAedes [TaxID: 7158]
Atelerix albiventris (Middle-African hedgehog) (Four-toed hedgehog) [TaxID: 9368]
Culex tritaeniorhynchus (Mosquito) [TaxID: 7178]
Halcyon [TaxID: 170865]
Homo sapiens (Human) [TaxID: 9606]
Quelea [TaxID: 158617]
Rhipicephalus [TaxID: 34630]
Proteomesi
  • UP000000570 Componenti: Genome

Subcellular locationi

Capsid protein :

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini268 – 701434ExtracellularSequence analysisAdd
BLAST
Transmembranei702 – 72221HelicalSequence analysisAdd
BLAST
Topological domaini723 – 75533CytoplasmicSequence analysisAdd
BLAST
Topological domaini756 – 77015ExtracellularSequence analysisAdd
BLAST
Transmembranei771 – 79121HelicalSequence analysisAdd
BLAST
Topological domaini792 – 7921CytoplasmicSequence analysis
Transmembranei793 – 81321HelicalSequence analysisAdd
BLAST
Topological domaini814 – 1230417ExtracellularSequence analysisAdd
BLAST
Transmembranei1231 – 125121HelicalSequence analysisAdd
BLAST
Topological domaini1252 – 12532CytoplasmicSequence analysis

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host cytoplasm, Host membrane, Membrane, T=4 icosahedral capsid protein, Viral envelope protein, Virion

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi219 – 2202SG → RST: Loss of autocatalytic cleavage by capsid protein. 1 Publication
Mutagenesisi267 – 2671W → A or R: Complete loss of cleavage by capsid protease.
Mutagenesisi330 – 3301R → S: Complete loss of p62 precursor processing. 1 Publication
Mutagenesisi333 – 3331R → F: Complete loss of p62 precursor processing. 1 Publication
Mutagenesisi755 – 7551A → F: Complete loss of p62 precursor-6K cleavage. 1 Publication
Mutagenesisi815 – 8151A → F: Complete loss of 6K protein-E1 envelope glycoprotein cleavage. 1 Publication
Mutagenesisi859 – 8591L → F: E1 fusion is less cholesterol and sphingolipid dependent. 1 Publication
Mutagenesisi890 – 8901D → A: Shifts the pH threshold for fusion to a more acidic range. 1 Publication
Mutagenesisi894 – 8941K → Q: No effect on E1 fusion activity. 1 Publication
Mutagenesisi898 – 8981G → A: Shifts the pH threshold for fusion to a more acidic range. 2 Publications
Mutagenesisi898 – 8981G → D: No effect on E1 fusion activity. 2 Publications
Mutagenesisi901 – 9011P → D: Retention of E1 protein in endoplasmic reticulum. 1 Publication
Mutagenesisi903 – 9031M → L: No effect on E1 fusion activity. 1 Publication
Mutagenesisi906 – 9061G → A: Shifts the pH threshold for fusion to a more acidic range. 2 Publications
Mutagenesisi906 – 9061G → D: Complete loss of E1 fusion activity. 2 Publications
Mutagenesisi906 – 9061G → P: Retention of E1 protein in endoplasmic reticulum. 2 Publications
Mutagenesisi993 – 9931V → A: E1 fusion is less cholesterol and sphingolipid dependent. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 267267Capsid proteinPRO_0000041311Add
BLAST
Chaini268 – 755488p62PRO_0000226237Add
BLAST
Chaini268 – 33366Protein E3PRO_0000041312Add
BLAST
Chaini334 – 755422Envelope glycoprotein E2PRO_0000041313Add
BLAST
Chaini756 – 81560Protein 6KPRO_0000041314Add
BLAST
Chaini816 – 1253438Envelope glycoprotein E1PRO_0000041315Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi119 ↔ 134
Glycosylationi280 – 2801N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi327 – 3271N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi533 – 5331N-linked (GlcNAc...); by hostSequence analysis
Glycosylationi595 – 5951N-linked (GlcNAc...); by hostSequence analysis
Lipidationi718 – 7181S-palmitoyl cysteine; by hostSequence analysis
Lipidationi728 – 7281S-palmitoyl cysteine; by hostBy similarity
Lipidationi748 – 7481S-palmitoyl cysteine; by hostBy similarity
Lipidationi749 – 7491S-palmitoyl cysteine; by hostBy similarity
Disulfide bondi864 ↔ 929
Disulfide bondi877 ↔ 909
Disulfide bondi878 ↔ 911
Disulfide bondi883 ↔ 893
Glycosylationi956 – 9561N-linked (GlcNAc...); by host2 Publications
Disulfide bondi1074 ↔ 1086
Disulfide bondi1116 ↔ 1191
Disulfide bondi1121 ↔ 1195
Disulfide bondi1143 ↔ 1185
Lipidationi1248 – 12481S-stearoyl cysteine; by host1 Publication

Post-translational modificationi

Specific enzymatic cleavages in vivo yield mature proteins. Capsid protein is auto-cleaved during polyprotein translation, unmasking p62 signal peptide. The remaining polyprotein is then targeted to the endoplasmic reticulum, where host signal peptidase cleaves it into p62, 6K and E1 proteins. p62 is further processed to mature E3 and E2 by host furin in trans-Golgi vesicle. Protein processing process takes about 30 minutes at physiologic temperatures. The folding of the p62/6K/E1 precursor requires the formation of intrachain disulfide bonds and has been shown to involve a transient covalent interaction between the nascent and newly synthesized heterodimer and the host-cell chaperones, P4HB/PDI and PDIA3/ERp57. The folding pathway also includes non covalent interaction with human CANX/calnexin and CALR/calreticulin.3 Publications
Envelope E1, E2 and E3 proteins are N-glycosylated.1 Publication
E2 is palmitoylated via thioester bonds. These palmitoylations may induce disruption of the C-terminus transmembrane. This would result in the reorientation of E2 c-terminus from lumenal to cytoplasmic side. 6K protein is also palmitoylated with about four covalently bound fatty acids per molecule. E1 is stearoylated.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei267 – 2682Cleavage; by capsid protein
Sitei333 – 3342Cleavage; by host furin
Sitei755 – 7562Cleavage; by host signal peptidase
Sitei815 – 8162Cleavage; by host signal peptidase

Keywords - PTMi

Autocatalytic cleavage, Cleavage on pair of basic residues, Disulfide bond, Glycoprotein, Lipoprotein, Palmitate

PTM databases

SwissPalmiP03315.
UniCarbKBiP03315.

Interactioni

Subunit structurei

p62 and E1 form a heterodimer shortly after synthesis. Processing of p62 into E2 and E3 results in a heterodimer of E2 and E1. Spike at virion surface are constituted of three E2-E1 heterodimers. After target cell attachment and endocytosis, E1 change conformation to form homotrimers.

Structurei

Secondary structure

1
1253
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi120 – 1256Combined sources
Beta strandi128 – 1347Combined sources
Beta strandi139 – 1413Combined sources
Beta strandi148 – 1525Combined sources
Helixi153 – 1564Combined sources
Beta strandi161 – 1633Combined sources
Turni164 – 1674Combined sources
Beta strandi168 – 1725Combined sources
Helixi175 – 1806Combined sources
Beta strandi190 – 1956Combined sources
Beta strandi198 – 2036Combined sources
Beta strandi206 – 2105Combined sources
Beta strandi222 – 2243Combined sources
Beta strandi230 – 23910Combined sources
Beta strandi241 – 25111Combined sources
Beta strandi253 – 2597Combined sources
Beta strandi821 – 8233Combined sources
Beta strandi830 – 8323Combined sources
Beta strandi837 – 8393Combined sources
Beta strandi844 – 86320Combined sources
Beta strandi866 – 8694Combined sources
Beta strandi874 – 8763Combined sources
Beta strandi892 – 8987Combined sources
Helixi903 – 9075Combined sources
Beta strandi910 – 9134Combined sources
Beta strandi916 – 92510Combined sources
Turni927 – 9315Combined sources
Beta strandi934 – 95421Combined sources
Beta strandi958 – 9625Combined sources
Beta strandi964 – 9663Combined sources
Beta strandi969 – 9713Combined sources
Beta strandi974 – 9785Combined sources
Beta strandi990 – 9945Combined sources
Beta strandi999 – 10013Combined sources
Helixi1007 – 10093Combined sources
Beta strandi1017 – 10248Combined sources
Beta strandi1041 – 10433Combined sources
Helixi1054 – 10618Combined sources
Helixi1066 – 10683Combined sources
Helixi1071 – 10733Combined sources
Beta strandi1075 – 10773Combined sources
Turni1078 – 10814Combined sources
Beta strandi1082 – 10843Combined sources
Beta strandi1089 – 10968Combined sources
Helixi1099 – 11013Combined sources
Turni1105 – 11073Combined sources
Beta strandi1111 – 112212Combined sources
Beta strandi1124 – 113916Combined sources
Beta strandi1141 – 11466Combined sources
Beta strandi1150 – 116112Combined sources
Beta strandi1166 – 11749Combined sources
Beta strandi1179 – 11846Combined sources
Beta strandi1187 – 11926Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DYLelectron microscopy9.00A/B/C/D119-267[»]
1I9WX-ray3.00A816-1205[»]
1RERX-ray3.20A/B/C816-1206[»]
1VCPX-ray3.00A/B/C119-267[»]
1VCQX-ray3.10A/B119-267[»]
2ALAX-ray3.00A816-1206[»]
2V33X-ray1.55A/B1107-1197[»]
ProteinModelPortaliP03315.
SMRiP03315. Positions 119-267, 816-1206.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP03315.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini119 – 267149Peptidase S3PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 113113Intrinsically disordered, in contact with genomic RNA in nucleocapsidSequence analysisAdd
BLAST
Regioni94 – 10613Ribosome-bindingAdd
BLAST
Regioni728 – 74821Transient transmembrane before p62-6K protein processingSequence analysisAdd
BLAST
Regioni899 – 91618E1 fusion peptide loopAdd
BLAST

Sequence similaritiesi

Contains 1 peptidase S3 domain.PROSITE-ProRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

KOiK19288.

Family and domain databases

Gene3Di2.60.40.350. 1 hit.
2.60.98.10. 3 hits.
InterProiIPR002548. Alpha_E1_glycop.
IPR000936. Alpha_E2_glycop.
IPR002533. Alpha_E3_glycop.
IPR000336. Flavivir/Alphavir_Ig-like.
IPR011998. Glycoprot_cen/dimer.
IPR013754. GlyE_dim.
IPR014756. Ig_E-set.
IPR009003. Peptidase_S1_PA.
IPR000930. Peptidase_S3.
[Graphical view]
PfamiPF01589. Alpha_E1_glycop. 1 hit.
PF00943. Alpha_E2_glycop. 1 hit.
PF01563. Alpha_E3_glycop. 1 hit.
PF00944. Peptidase_S3. 1 hit.
[Graphical view]
PRINTSiPR00798. TOGAVIRIN.
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF56983. SSF56983. 1 hit.
SSF81296. SSF81296. 1 hit.
PROSITEiPS51690. ALPHAVIRUS_CP. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. AlignAdd to basket

Isoform Structural polyprotein (identifier: P03315-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MNYIPTQTFY GRRWRPRPAA RPWPLQATPV APVVPDFQAQ QMQQLISAVN
60 70 80 90 100
ALTMRQNAIA PARPPKPKKK KTTKPKPKTQ PKKINGKTQQ QKKKDKQADK
110 120 130 140 150
KKKKPGKRER MCMKIENDCI FEVKHEGKVT GYACLVGDKV MKPAHVKGVI
160 170 180 190 200
DNADLAKLAF KKSSKYDLEC AQIPVHMRSD ASKYTHEKPE GHYNWHHGAV
210 220 230 240 250
QYSGGRFTIP TGAGKPGDSG RPIFDNKGRV VAIVLGGANE GSRTALSVVT
260 270 280 290 300
WNKDMVTRVT PEGSEEWSAP LITAMCVLAN ATFPCFQPPC VPCCYENNAE
310 320 330 340 350
ATLRMLEDNV DRPGYYDLLQ AALTCRNGTR HRRSVSQHFN VYKATRPYIA
360 370 380 390 400
YCADCGAGHS CHSPVAIEAV RSEATDGMLK IQFSAQIGID KSDNHDYTKI
410 420 430 440 450
RYADGHAIEN AVRSSLKVAT SGDCFVHGTM GHFILAKCPP GEFLQVSIQD
460 470 480 490 500
TRNAVRACRI QYHHDPQPVG REKFTIRPHY GKEIPCTTYQ QTTAETVEEI
510 520 530 540 550
DMHMPPDTPD RTLLSQQSGN VKITVGGKKV KYNCTCGTGN VGTTNSDMTI
560 570 580 590 600
NTCLIEQCHV SVTDHKKWQF NSPFVPRADE PARKGKVHIP FPLDNITCRV
610 620 630 640 650
PMAREPTVIH GKREVTLHLH PDHPTLFSYR TLGEDPQYHE EWVTAAVERT
660 670 680 690 700
IPVPVDGMEY HWGNNDPVRL WSQLTTEGKP HGWPHQIVQY YYGLYPAATV
710 720 730 740 750
SAVVGMSLLA LISIFASCYM LVAARSKCLT PYALTPGAAV PWTLGILCCA
760 770 780 790 800
PRAHAASVAE TMAYLWDQNQ ALFWLEFAAP VACILIITYC LRNVLCCCKS
810 820 830 840 850
LSFLVLLSLG ATARAYEHST VMPNVVGFPY KAHIERPGYS PLTLQMQVVE
860 870 880 890 900
TSLEPTLNLE YITCEYKTVV PSPYVKCCGA SECSTKEKPD YQCKVYTGVY
910 920 930 940 950
PFMWGGAYCF CDSENTQLSE AYVDRSDVCR HDHASAYKAH TASLKAKVRV
960 970 980 990 1000
MYGNVNQTVD VYVNGDHAVT IGGTQFIFGP LSSAWTPFDN KIVVYKDEVF
1010 1020 1030 1040 1050
NQDFPPYGSG QPGRFGDIQS RTVESNDLYA NTALKLARPS PGMVHVPYTQ
1060 1070 1080 1090 1100
TPSGFKYWLK EKGTALNTKA PFGCQIKTNP VRAMNCAVGN IPVSMNLPDS
1110 1120 1130 1140 1150
AFTRIVEAPT IIDLTCTVAT CTHSSDFGGV LTLTYKTNKN GDCSVHSHSN
1160 1170 1180 1190 1200
VATLQEATAK VKTAGKVTLH FSTASASPSF VVSLCSARAT CSASCEPPKD
1210 1220 1230 1240 1250
HIVPYAASHS NVVFPDMSGT ALSWVQKISG GLGAFAIGAI LVLVVVTCIG

LRR
Note: Produced by conventional translation.
Length:1,253
Mass (Da):138,017
Last modified:July 21, 1986 - v1
Checksum:i2A73228D08B82AC5
GO
Isoform Frameshifted structural polyprotein (identifier: P0DJZ6-1) [UniParc]FASTAAdd to basket

The sequence of this isoform can be found in the external entry P0DJZ6.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by -1 ribosomal frameshifting in Protein 6K ORF.
Length:830
Mass (Da):92,349
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti62 – 621A → T in strain: A7.
Natural varianti63 – 631R → G in strain: L10.
Natural varianti85 – 851N → K in strain: A7, L10 and MTV.
Natural varianti279 – 2791A → T in strain: A7.
Natural varianti291 – 2911V → A in strain: A7.
Natural varianti370 – 3701V → I in strain: A7, L10 and MTV.
Natural varianti437 – 4371K → T in strain: A7, L10 and MTV.
Natural varianti545 – 5451N → S in strain: A7.
Natural varianti548 – 5481M → K in strain: A7 and MTV.
Natural varianti614 – 6141E → K in strain: MTV.
Natural varianti700 – 7001V → A in strain: A7.
Natural varianti704 – 7041V → A in strain: A7.
Natural varianti722 – 7221V → A in strain: A7 and MTV.
Natural varianti880 – 8801A → S in strain: A7.
Natural varianti930 – 9301R → K in strain: A7.
Natural varianti1043 – 10431M → T in strain: A7 and MTV.
Natural varianti1112 – 11121I → T in strain: A7 and MTV.
Natural varianti1134 – 11341T → K in strain: A7.
Natural varianti1138 – 11381N → D in strain: A7, L10 and MTV.
Natural varianti1165 – 11651G → R in strain: MTV.
Natural varianti1188 – 11881R → K in strain: A7 and MTV.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48163 Genomic RNA. Translation: CAD90834.1.
EU350586 Genomic RNA. Translation: ACB12688.1.
AY112987 Genomic RNA. Translation: AAM64227.1.
X04129 Genomic RNA. Translation: CAA27742.1.
PIRiA93861. VHWV.
S42462.
RefSeqiNP_463458.1. NC_003215.1. [P03315-1]

Genome annotation databases

GeneIDi922351.
KEGGivg:922351.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Web resourcesi

Virus Particle ExploreR db

Icosahedral capsid structure

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48163 Genomic RNA. Translation: CAD90834.1.
EU350586 Genomic RNA. Translation: ACB12688.1.
AY112987 Genomic RNA. Translation: AAM64227.1.
X04129 Genomic RNA. Translation: CAA27742.1.
PIRiA93861. VHWV.
S42462.
RefSeqiNP_463458.1. NC_003215.1. [P03315-1]

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DYLelectron microscopy9.00A/B/C/D119-267[»]
1I9WX-ray3.00A816-1205[»]
1RERX-ray3.20A/B/C816-1206[»]
1VCPX-ray3.00A/B/C119-267[»]
1VCQX-ray3.10A/B119-267[»]
2ALAX-ray3.00A816-1206[»]
2V33X-ray1.55A/B1107-1197[»]
ProteinModelPortaliP03315.
SMRiP03315. Positions 119-267, 816-1206.
ModBaseiSearch...
MobiDBiSearch...

Protein family/group databases

MEROPSiS03.001.
TCDBi1.G.4.1.1. the viral pore-forming membrane fusion protein-4 (vmfp4) family.

PTM databases

SwissPalmiP03315.
UniCarbKBiP03315.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi922351.
KEGGivg:922351.

Phylogenomic databases

KOiK19288.

Miscellaneous databases

EvolutionaryTraceiP03315.

Family and domain databases

Gene3Di2.60.40.350. 1 hit.
2.60.98.10. 3 hits.
InterProiIPR002548. Alpha_E1_glycop.
IPR000936. Alpha_E2_glycop.
IPR002533. Alpha_E3_glycop.
IPR000336. Flavivir/Alphavir_Ig-like.
IPR011998. Glycoprot_cen/dimer.
IPR013754. GlyE_dim.
IPR014756. Ig_E-set.
IPR009003. Peptidase_S1_PA.
IPR000930. Peptidase_S3.
[Graphical view]
PfamiPF01589. Alpha_E1_glycop. 1 hit.
PF00943. Alpha_E2_glycop. 1 hit.
PF01563. Alpha_E3_glycop. 1 hit.
PF00944. Peptidase_S3. 1 hit.
[Graphical view]
PRINTSiPR00798. TOGAVIRIN.
SUPFAMiSSF50494. SSF50494. 1 hit.
SSF56983. SSF56983. 1 hit.
SSF81296. SSF81296. 1 hit.
PROSITEiPS51690. ALPHAVIRUS_CP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Sequence analysis of the avirulent, demyelinating A7 strain of Semliki Forest virus."
    Tarbatt C.J., Glasgow G.M., Mooney D.A., Sheahan B.J., Atkins G.J.
    J. Gen. Virol. 78:1551-1557(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: A7.
  2. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: MTV.
  3. "Semliki Forest Virus - L10 Strain Complete Genome."
    Logue C., Mooney D., Shanley R., Atkins G.J.
    Submitted (MAY-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
    Strain: L10.
  4. "The capsid protein of Semliki Forest virus has clusters of basic amino acids and prolines in its amino-terminal region."
    Garoff H., Frischauf A.-M., Simons K., Lehrach H., Delius H.
    Proc. Natl. Acad. Sci. U.S.A. 77:6376-6380(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1-305.
  5. "Nucleotide sequence of cDNA coding for Semliki Forest virus membrane glycoproteins."
    Garoff H., Frischauf A.-M., Simons K., Lehrach H., Delius H.
    Nature 288:236-241(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 266-1253.
  6. "An evolutionary tree relating eight alphaviruses, based on amino-terminal sequences of their glycoproteins."
    Bell J.R., Kinney R.M., Trent D.W., Strauss E.G., Strauss J.H.
    Proc. Natl. Acad. Sci. U.S.A. 81:4702-4706(1984) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 334-402 AND 816-881.
  7. "Carboxyl-terminal sequence analysis of the four structural proteins of Semliki Forest virus."
    Kalkkinen N.
    FEBS Lett. 115:163-166(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE.
  8. "Processing of the Semliki Forest virus structural polyprotein: role of the capsid protease."
    Melancon P., Garoff H.
    J. Virol. 61:1301-1309(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION (CAPSID PROTEIN), AUTOCATALYTIC CLEAVAGE BY CAPSID PROTEIN, MUTAGENESIS OF 219-SER-GLY-220.
  9. "Chemical identification of cysteine as palmitoylation site in a transmembrane protein (Semliki Forest virus E1)."
    Schmidt M., Schmidt M.F., Rott R.
    J. Biol. Chem. 263:18635-18639(1988) [PubMed] [Europe PMC] [Abstract]
    Cited for: STEAROYLATION AT CYS-1248, PALMITOYLATION.
  10. "The cytoplasmic domain of alphavirus E2 glycoprotein contains a short linear recognition signal required for viral budding."
    Kail M., Hollinshead M., Ansorge W., Pepperkok R., Frank R., Griffiths G., Vaux D.
    EMBO J. 10:2343-2351(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION (ENVELOPE GLYCOPROTEIN E2).
  11. "Processing of the p62 envelope precursor protein of Semliki Forest virus."
    Jain S.K., DeCandido S., Kielian M.
    J. Biol. Chem. 266:5756-5761(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: CLEAVAGE SITE OF P62, MUTAGENESIS OF ARG-330 AND ARG-333.
  12. "Mutagenesis of the putative fusion domain of the Semliki Forest virus spike protein."
    Levy-Mintz P., Kielian M.
    J. Virol. 65:4292-4300(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ASP-890; LYS-894; GLY-898; PRO-901; MET-903 AND GLY-906.
  13. "Internally located cleavable signal sequences direct the formation of Semliki Forest virus membrane proteins from a polyprotein precursor."
    Liljestrom P., Garoff H.
    J. Virol. 65:147-154(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: CLEAVAGE BY SIGNAL PEPTIDASE, MUTAGENESIS OF ALA-755 AND ALA-815.
  14. "Fate of the 6K membrane protein of Semliki Forest virus during virus assembly."
    Lusa S., Garoff H., Liljestrom P.
    Virology 185:843-846(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION (PROTEIN 6K).
  15. "Membrane fusion of Semliki Forest virus involves homotrimers of the fusion protein."
    Wahlberg J.M., Bron R., Wilschut J., Garoff H.
    J. Virol. 66:7309-7318(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION (ENVELOPE GLYCOPROTEIN E1).
  16. "The 6-kilodalton membrane protein of Semliki Forest virus is involved in the budding process."
    Loewy A., Smyth J., von Bonsdorff C.H., Liljestrom P., Schlesinger M.J.
    J. Virol. 69:469-475(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION (PROTEIN 6K).
  17. "A single point mutation controls the cholesterol dependence of Semliki Forest virus entry and exit."
    Vashishtha M., Phalen T., Marquardt M.T., Ryu J.S., Ng A.C., Kielian M.
    J. Cell Biol. 140:91-99(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF GLY-898 AND GLY-906.
  18. "Role of the C-terminal tryptophan residue for the structure-function of the alphavirus capsid protein."
    Skoging U., Liljestrom P.
    J. Mol. Biol. 279:865-872(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION (CAPSID PROTEIN), AUTOCATALYTIC CLEAVAGE BY CAPSID PROTEIN.
  19. "Glycoproteins form mixed disulphides with oxidoreductases during folding in living cells."
    Molinari M., Helenius A.
    Nature 402:90-93(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH HUMAN CHAPERONES P4HB/PDI AND PDIA3/ERP57.
  20. "Novel mutations that control the sphingolipid and cholesterol dependence of the Semliki Forest virus fusion protein."
    Chatterjee P.K., Eng C.H., Kielian M.
    J. Virol. 76:12712-12722(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF LEU-859 AND VAL-993.
  21. "Furin processing and proteolytic activation of Semliki Forest virus."
    Zhang X., Fugere M., Day R., Kielian M.
    J. Virol. 77:2981-2989(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEOLYTIC PROCESSING OF P62 BY HOST FURIN.
  22. "Rab7 associates with early endosomes to mediate sorting and transport of Semliki forest virus to late endosomes."
    Vonderheit A., Helenius A.
    PLoS Biol. 3:E233-E233(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  23. "Structure of Semliki Forest virus core protein."
    Choi H.-K., Lu G., Lee S., Wengler G., Rossmann M.G.
    Proteins 27:345-359(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 119-267.
  24. "Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus."
    Mancini E.J., Clarke M., Gowen B.E., Rutten T., Fuller S.D.
    Mol. Cell 5:255-266(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY ELECTRON MICROSCOPY (9.0 ANGSTROMS) OF 119-267, DISULFIDE BONDS.
  25. "The Fusion glycoprotein shell of Semliki Forest virus: an icosahedral assembly primed for fusogenic activation at endosomal pH."
    Lescar J., Roussel A., Wien M.W., Navaza J., Fuller S.D., Wengler G., Wengler G., Rey F.A.
    Cell 105:137-148(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 816-1205.
  26. "Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus."
    Gibbons D.L., Vaney M.C., Roussel A., Vigouroux A., Reilly B., Lepault J., Kielian M., Rey F.A.
    Nature 427:320-325(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF 816-1206, GLYCOSYLATION AT ASN-956, DISULFIDE BONDS.
  27. "The role of E3 in pH protection during alphavirus assembly and exit."
    Uchime O., Fields W., Kielian M.
    J. Virol. 87:10255-10262(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION (PROTEIN E3).

Entry informationi

Entry nameiPOLS_SFV
AccessioniPrimary (citable) accession number: P03315
Secondary accession number(s): B3TP01, Q809B6, Q8JMP5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: February 17, 2016
This is version 145 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

The mature virion nucleocapsid consists of 240 copies of the capsid protein. 80 spike trimers of E1 and E2 are present at the surface of mature virion. They project about 100 Angstroms from the outer surface and are located at the local and strict three fold axis of the icosaedral lattice. The glycoproteins splay out to form a protein shell or skirt covering most of the outer surface of the membrane bilayer.
Structural polyprotein is translated from a subgenomic RNA synthesized during togavirus replication.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Peptidase families
    Classification of peptidase families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.