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Protein

Outer capsid protein sigma-1

Gene

S1

Organism
Reovirus type 1 (strain Lang) (T1L) (Mammalian orthoreovirus 1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Fiber-like molecule that attaches the virion to the host cell membrane by binding to the primary receptor F11R/JAM-A and to sialic acid containing proteins (coreceptor). The interaction of sigma-1 with F11R is required for NF-kB activation and apoptosis. Binding to both sialic acid and F11R is required to induce maximal levels of apoptosis (By similarity).By similarity

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hemagglutinin

Keywords - Biological processi

Host-virus interaction, Viral attachment to host cell, Virus entry into host cell

Names & Taxonomyi

Protein namesi
Recommended name:
Outer capsid protein sigma-1
Short name:
Sigma1
Alternative name(s):
Cell attachment protein
Hemagglutinin
Gene namesi
Name:S1
OrganismiReovirus type 1 (strain Lang) (T1L) (Mammalian orthoreovirus 1)
Taxonomic identifieri10884 [NCBI]
Taxonomic lineageiVirusesdsRNA virusesReoviridaeSpinareovirinaeOrthoreovirus
Virus hostiMammalia [TaxID: 40674]
Proteomesi
  • UP000007253 Componenti: Genome

Subcellular locationi

  • Virion By similarity

  • Note: Found in the outer capsid (36 copies).By similarity

GO - Cellular componenti

  • viral capsid Source: CACAO
  • viral outer capsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Outer capsid protein, Virion

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000406671 – 470Outer capsid protein sigma-1Add BLAST470

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi21N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi121N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi205N-linked (GlcNAc...); by hostSequence analysis1
Glycosylationi353N-linked (GlcNAc...); by hostSequence analysis1

Post-translational modificationi

Undergoes dramatic conformational rearrangements during viral disassembly in the endocytic pathway.By similarity

Keywords - PTMi

Glycoprotein

Interactioni

Subunit structurei

Homotrimer. Interacts (via the head region) with human F11R (By similarity).By similarity

Structurei

Secondary structure

1470
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi274 – 278Combined sources5
Beta strandi281 – 285Combined sources5
Turni290 – 292Combined sources3
Beta strandi293 – 296Combined sources4
Beta strandi299 – 304Combined sources6
Beta strandi315 – 318Combined sources4
Turni319 – 322Combined sources4
Beta strandi323 – 326Combined sources4
Helixi328 – 331Combined sources4
Beta strandi333 – 345Combined sources13
Beta strandi348 – 361Combined sources14
Beta strandi364 – 369Combined sources6
Beta strandi372 – 375Combined sources4
Beta strandi379 – 386Combined sources8
Turni387 – 390Combined sources4
Helixi397 – 400Combined sources4
Beta strandi409 – 420Combined sources12
Beta strandi423 – 437Combined sources15
Beta strandi440 – 449Combined sources10
Beta strandi454 – 458Combined sources5
Beta strandi461 – 466Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4GU3X-ray3.60A/B/C261-470[»]
4GU4X-ray3.50A/B/C261-470[»]
4ODBX-ray3.20A/B/C308-470[»]
4XC5X-ray2.20A/B/C308-470[»]
ProteinModelPortaliP04506.
SMRiP04506.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 324TailAdd BLAST324
Regioni325 – 470HeadAdd BLAST146

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili26 – 46Sequence analysisAdd BLAST21

Sequence similaritiesi

Keywords - Domaini

Coiled coil

Family and domain databases

Gene3Di2.10.25.20. 1 hit.
2.60.90.20. 1 hit.
InterProiIPR008982. Adenovirus_pIV-rel_att.
IPR009013. Attachment_protein_shaft_dom.
IPR027314. Sigma1_globular_dom.
IPR002592. Vir_attach_sigma1_reovir.
[Graphical view]
PfamiPF01664. Reo_sigma1. 1 hit.
[Graphical view]
SUPFAMiSSF49835. SSF49835. 1 hit.

Sequencei

Sequence statusi: Complete.

P04506-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDASLITEIR KIVLQLSVSS NGSQSKEIEE IKKQVQVNVD DIRAANIKLD
60 70 80 90 100
GLGRQIADIS NSISTIESRL GEMDNRLVGI SSQVTQLSNS VSQNTQSISS
110 120 130 140 150
LGDRINAVEP RVDSLDTVTS NLTGRTSTLE ADVGSLRTEL AALTTRVTTE
160 170 180 190 200
VTRLDGLINS GQNSIGELST RLSNVETSMV TTAGRGLQKN GNTLNVIVGN
210 220 230 240 250
GMWFNSSNQL QLDLSGQSKG VGFVGTGMVV KIDTNYFAYN SNGEITLVSQ
260 270 280 290 300
INELPSRVST LESAKIDSVL PPLTVREASG VRTLSFGYDT SDFTIINSVL
310 320 330 340 350
SLRSRLTLPT YRYPLELDTA NNRVQVADRF GMRTGTWTGQ LQYQHPQLSW
360 370 380 390 400
RANVTLNLMK VDDWLVLSFS QMTTNSIMAD GKFVINFVSG LSSGWQTGDT
410 420 430 440 450
EPSSTIDPLS TTFAAVQFLN NGQRIDAFRI MGVSEWTDGE LEIKNYGGTY
460 470
TGHTQVYWAP WTIMYPCNVR
Length:470
Mass (Da):51,404
Last modified:November 1, 1990 - v2
Checksum:iF4D18989AD54491C
GO

Sequence cautioni

The sequence AAA47276 differs from that shown. Reason: Frameshift at position 410.Curated
The sequence AAA66877 differs from that shown. Reason: Frameshift at positions 410 and 434.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti91V → G in AAA66877 (PubMed:3855545).Curated1
Sequence conflicti91V → G in AAA47276 (PubMed:2430568).Curated1
Sequence conflicti169S → F in AAA66877 (PubMed:3855545).Curated1
Sequence conflicti384V → L in AAA47276 (PubMed:2430568).Curated1
Sequence conflicti409L → W in AAA47242 (PubMed:2335823).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M10260 Genomic RNA. Translation: AAA66877.1. Frameshift.
M14779 Genomic RNA. Translation: AAA47276.1. Frameshift.
M32860 Genomic RNA. Translation: AAA47267.1.
M35963 Genomic RNA. Translation: AAA47242.1.
EF494445 Genomic RNA. Translation: ABP48923.1.
AH002406 Genomic RNA. Translation: AAA47240.1.
PIRiA04122. HMXRH1.
A34829. HMXRL1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M10260 Genomic RNA. Translation: AAA66877.1. Frameshift.
M14779 Genomic RNA. Translation: AAA47276.1. Frameshift.
M32860 Genomic RNA. Translation: AAA47267.1.
M35963 Genomic RNA. Translation: AAA47242.1.
EF494445 Genomic RNA. Translation: ABP48923.1.
AH002406 Genomic RNA. Translation: AAA47240.1.
PIRiA04122. HMXRH1.
A34829. HMXRL1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4GU3X-ray3.60A/B/C261-470[»]
4GU4X-ray3.50A/B/C261-470[»]
4ODBX-ray3.20A/B/C308-470[»]
4XC5X-ray2.20A/B/C308-470[»]
ProteinModelPortaliP04506.
SMRiP04506.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Family and domain databases

Gene3Di2.10.25.20. 1 hit.
2.60.90.20. 1 hit.
InterProiIPR008982. Adenovirus_pIV-rel_att.
IPR009013. Attachment_protein_shaft_dom.
IPR027314. Sigma1_globular_dom.
IPR002592. Vir_attach_sigma1_reovir.
[Graphical view]
PfamiPF01664. Reo_sigma1. 1 hit.
[Graphical view]
SUPFAMiSSF49835. SSF49835. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiSIGM1_REOVL
AccessioniPrimary (citable) accession number: P04506
Secondary accession number(s): A4ZY30, P07937
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: November 1, 1990
Last modified: November 2, 2016
This is version 94 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.