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Protein

Structural polyprotein

Gene
N/A
Organism
Barmah forest virus (BFV)
Status
Reviewed-Annotation score: -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 icosahedric core particles. The resulting nucleocapsid eventually associates with the cytoplasmic domain of the spike glycoprotein E2 at the cell membrane, leading to budding and formation of mature virions. In case of infection, 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.By similarity
Assembly protein E3: Provides the signal sequence for the translocation of the precursor of protein E3/E2 to the host endoplasmic reticulum. Mediates pH protection of spike glycoprotein E1 during the transport via the secretory pathway.By similarity
Spike 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.By similarity
6K protein: 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.By similarity
Spike 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.By similarity

Miscellaneous

Structural polyprotein: Translated from a subgenomic RNA synthesized during togavirus replication.By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei131Charge relay systemPROSITE-ProRule annotation1
Active sitei153Charge relay systemPROSITE-ProRule annotation1
Active sitei205Charge relay systemPROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionHydrolase, Protease, Serine protease
Biological processFusion 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 entry into host cell

Protein family/group databases

MEROPSiS03.001
TCDBi1.G.4.1.3 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):
p62
pE2
Alternative name(s):
E2 envelope glycoprotein
Alternative name(s):
E1 envelope glycoprotein
OrganismiBarmah forest virus (BFV)
Taxonomic identifieri11020 [NCBI]
Taxonomic lineageiVirusesssRNA virusesssRNA positive-strand viruses, no DNA stageTogaviridaeAlphavirus
Virus hostiAnopheles amictus [TaxID: 59117]
Culex annulirostris (Common banded mosquito) [TaxID: 162997]
Homo sapiens (Human) [TaxID: 9606]
Macropus [TaxID: 9312]
Proteomesi
  • UP000007609 Componenti: Genome

Subcellular locationi

Capsid protein :
  • Virion By similarity
  • Host cytoplasm By similarity
  • Host cell membrane By similarity
Spike glycoprotein E2 :
6K protein :
Spike glycoprotein E1 :

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini322 – 686ExtracellularSequence analysisAdd BLAST365
Transmembranei687 – 707HelicalSequence analysisAdd BLAST21
Topological domaini708 – 751CytoplasmicSequence analysisAdd BLAST44
Topological domaini752 – 756ExtracellularSequence analysis5
Transmembranei757 – 777HelicalSequence analysisAdd BLAST21
Topological domaini778 – 779CytoplasmicSequence analysis2
Transmembranei780 – 800HelicalSequence analysisAdd BLAST21
Topological domaini801 – 1216ExtracellularSequence analysisAdd BLAST416
Transmembranei1217 – 1237HelicalSequence analysisAdd BLAST21
Topological domaini1238 – 1239CytoplasmicSequence analysis2

GO - Cellular componenti

Keywords - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002387121 – 253Capsid proteinBy similarityAdd BLAST253
ChainiPRO_0000238713254 – 742Precursor of protein E3/E2By similarityAdd BLAST489
ChainiPRO_0000238714254 – 321Assembly protein E3By similarityAdd BLAST68
ChainiPRO_0000238715322 – 742Spike glycoprotein E2By similarityAdd BLAST421
ChainiPRO_0000238716743 – 8006K proteinBy similarityAdd BLAST58
ChainiPRO_0000238717801 – 1239Spike glycoprotein E1By similarityAdd BLAST439

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi268N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Lipidationi715S-palmitoyl cysteine; by hostBy similarity1
Lipidationi735S-palmitoyl cysteine; by hostBy similarity1
Lipidationi736S-palmitoyl cysteine; by hostBy similarity1
Disulfide bondi849 ↔ 914By similarity
Disulfide bondi862 ↔ 894By similarity
Disulfide bondi863 ↔ 896By similarity
Disulfide bondi868 ↔ 878By similarity
Glycosylationi941N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Glycosylationi1009N-linked (GlcNAc...) asparagine; by hostSequence analysis1
Disulfide bondi1059 ↔ 1071By similarity
Disulfide bondi1101 ↔ 1176By similarity
Disulfide bondi1106 ↔ 1180By similarity
Disulfide bondi1128 ↔ 1170By similarity

Post-translational modificationi

Structural polyprotein: Specific enzymatic cleavages in vivo yield mature proteins. Capsid protein is auto-cleaved during polyprotein translation, unmasking a signal peptide at the N-terminus of the precursor of E3/E2. The remaining polyprotein is then targeted to the host endoplasmic reticulum, where host signal peptidase cleaves it into pE2, 6K and E1 proteins. pE2 is further processed to mature E3 and E2 by host furin in trans-Golgi vesicle.By similarity
Spike glycoprotein E2: 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.By similarity
Spike glycoprotein E1: N-glycosylated.By similarity
Spike glycoprotein E2: N-glycosylated.By similarity
Assembly protein E3: N-glycosylated.By similarity
6K protein: Palmitoylated via thioester bonds.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei253 – 254Cleavage; by autolysisBy similarity2
Sitei321 – 322Cleavage; by host furinBy similarity2
Sitei742 – 743Cleavage; by host signal peptidaseBy similarity2
Sitei800 – 801Cleavage; by host signal peptidaseBy similarity2

Keywords - PTMi

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

Interactioni

Subunit structurei

Precursor of protein E3/E2: The precursor of protein E3/E2 and E1 form a heterodimer shortly after synthesis. Spike glycoprotein E1: The precursor of protein E3/E2 and E1 form a heterodimer shortly after synthesis. Spike glycoprotein E1: Processing of the precursor of protein E3/E2 into E2 and E3 results in a heterodimer of the spike glycoproteins E2 and E1. Spike glycoprotein E2: Processing of the precursor of protein E3/E2 into E2 and E3 results in a heterodimer of the spike glycoproteins E2 and E1. Spike glycoprotein E1: Spike at virion surface are constituted of three E2-E1 heterodimers. Spike glycoprotein E2: Spike at virion surface are constituted of three E2-E1 heterodimers. Spike glycoprotein E1: After target cell attachment and endocytosis, E1 change conformation to form homotrimers. 6K protein: Interacts with spike glycoprotein E1. 6K protein: Interacts with spike glycoprotein E2. Spike glycoprotein E1: Interacts with 6K protein. Spike glycoprotein E2: Interacts with 6K protein.By similarity

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YEWelectron microscopy5.00A/D/G/J1-253[»]
B/E/H/K804-1239[»]
C/F/I/L322-742[»]
ProteinModelPortaliP89946
SMRiP89946
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini105 – 253Peptidase S3PROSITE-ProRule annotationAdd BLAST149

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni254 – 269Functions as an uncleaved signal peptide for the precursor of protein E3/E2By similarityAdd BLAST16
Regioni884 – 901E1 fusion peptide loopBy similarityAdd BLAST18

Domaini

Structural polyprotein: As soon as the capsid protein has been autocleaved, an internal uncleaved signal peptide directs the remaining polyprotein to the endoplasmic reticulum.By similarity

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

KOiK19288
OrthoDBiVOG0900007W

Family and domain databases

Gene3Di2.60.40.350, 1 hit
2.60.98.10, 3 hits
InterProiView protein in InterPro
IPR002548 Alpha_E1_glycop
IPR000936 Alpha_E2_glycop
IPR002533 Alpha_E3_glycop
IPR000336 Flavivir/Alphavir_Ig-like_sf
IPR036253 Glycoprot_cen/dimer_sf
IPR038055 Glycoprot_E_dimer_dom
IPR014756 Ig_E-set
IPR009003 Peptidase_S1_PA
IPR000930 Peptidase_S3
PfamiView protein in Pfam
PF01589 Alpha_E1_glycop, 1 hit
PF00943 Alpha_E2_glycop, 1 hit
PF01563 Alpha_E3_glycop, 1 hit
PF00944 Peptidase_S3, 1 hit
PRINTSiPR00798 TOGAVIRIN
SUPFAMiSSF50494 SSF50494, 1 hit
SSF56983 SSF56983, 1 hit
SSF81296 SSF81296, 1 hit
PROSITEiView protein in PROSITE
PS51690 ALPHAVIRUS_CP, 1 hit

Sequencei

Sequence statusi: Complete.

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

P89946-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDFIPTQTFY GRRWRPAPVQ RYIPQPQPPA PPRRRRGPSQ LQQLVAALGA
60 70 80 90 100
LALQPKQKQK RAQKKPKKTP PPKPKKTQKP KKPTQKKKSK PGKRMRNCMK
110 120 130 140 150
IENDCIFPVM LDGKVNGYAC LVGDKVMKPA HVKGTIDNPE LAKLTFKKSS
160 170 180 190 200
KYDLECAQVP VCMKSDASKF THEKPEGHYN WHHGAVQFSN GRFTIPTGSG
210 220 230 240 250
KPGDSGRPIF DNTGKVVAIV LGGANEGART ALSVVTWNKD MVTRITPEES
260 270 280 290 300
VEWSAAALNI TALCVLQNLS FPCDAPPCAP CCYEKDPAGT LRLLSDHYYH
310 320 330 340 350
PKYYELLDST MHCPQGRRPK RSVAHFEAYK ATRPYIGWCA DCGLAGSCPS
360 370 380 390 400
PVSIEHVWSD ADDGVLKIQV SMQIGIAKSN TINHAKIRYM GANGVQEAER
410 420 430 440 450
STLSVSTTAP CDILATMGHF ILARCRPGSQ VEVSLSTDPK LLCRTPFSHK
460 470 480 490 500
PRFIGNEKSP APTGHKTRIP CKTYSHQTDL TREEITMHVP PDVPIQGLVS
510 520 530 540 550
NTGKSYSLDP KTKTIKYKCT CGETVKEGTA TNKITLFNCD TAPKCITYAV
560 570 580 590 600
DNTVWQYNSQ YVPRSEVTEV KGKIHVPFPL TDSTCAVSVA PEPQVTYRLG
610 620 630 640 650
EVEFHFHPMY PTLFSIRSLG KDPSHSQEWI DTPMSKTIQV GAEGVEYVWG
660 670 680 690 700
NNNPVRLWAQ KSSSSSAHGN PISIVSHYYD LYPYWTITVL ASLGLLIVIS
710 720 730 740 750
SGFSCFLCSV ARTKCLTPYQ LAPGAQLPTF IALLCCAKSA RADTLDDFSY
760 770 780 790 800
LWTNNQAMFW LQLASPVAAF LCLSYCCRNL ACCMKIFLGI SGLCVIATQA
810 820 830 840 850
YEHSTTMPNQ VGIPFKALIE RPGYAGLPLS LVVIKSELVP SLVQDYITCN
860 870 880 890 900
YKTVVPSPYI KCCGGAECSH KNEADYKCSV FTGVYPFMWG GAYCFCDTEN
910 920 930 940 950
SQMSEVYVTR GESCEADHAI AYQVHTASLK AQVMISIGEL NQTVDVFVNG
960 970 980 990 1000
DSPARIQQSK FILGPISSAW SPFDHKVIVY RDEVYNEDYA PYGSGQAGRF
1010 1020 1030 1040 1050
GDIQSRTVNS TDVYANTNLK LKRPASGNVH VPYTQTPSGF SYWKKEKGVP
1060 1070 1080 1090 1100
LNRNAPFGCI IKVNPVRAEN CVYGNIPISM DIADAHFTRI DESPSVSLKA
1110 1120 1130 1140 1150
CEVQSCTYSS DFGGVASISY TSNKVGKCAI HSHSNSATMK DSVQDVQESG
1160 1170 1180 1190 1200
ALSLFFATSS VEPNFVVQVC NARITCHGKC EPPKDHIVPY AAKHNDAEFP
1210 1220 1230
SISTTAWQWL AHTTSGPLTI LVVAIIVVVV VSIVVCARH
Length:1,239
Mass (Da):136,297
Last modified:May 30, 2006 - v2
Checksum:iE82B5BDA41BEACD5
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti826G → A. 1
Natural varianti1020K → R. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U73745 Genomic RNA Translation: AAB40702.1
AF339488 Genomic RNA Translation: AAO33347.1
PIRiC37264
D21774
RefSeqiNP_054024.1, NC_001786.1

Genome annotation databases

GeneIDi1489701
KEGGivg:1489701

Similar proteinsi

Entry informationi

Entry nameiPOLS_BFV
AccessioniPrimary (citable) accession number: P89946
Secondary accession number(s): Q80S23
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2006
Last sequence update: May 30, 2006
Last modified: March 28, 2018
This is version 110 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome
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Main funding by: National Institutes of Health