P04506 (SIGM1_REOVL) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Outer capsid protein sigma-1
Short name=Sigma1

Alternative name(s):
Cell attachment protein
Hemagglutinin

Gene names

Name:

S1

Organism

Reovirus type 1 (strain Lang) (T1L) (Mammalian orthoreovirus 1) [Reference proteome]

Taxonomic identifier

10884 [NCBI]

Taxonomic lineage

Viruses › dsRNA viruses › Reoviridae › Spinareovirinae › Orthoreovirus › Mammalian orthoreovirus › Mammalian orthoreovirus 1

Virus host

Mammalia [TaxID: 40674]

Protein attributes

Sequence length	470 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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.
Subunit structure	Homotrimer. Interacts (via the head region) with human F11R By similarity.
Subcellular location	Virion By similarity. Note: Found in the outer capsid (36 copies) By similarity.
Post-translational modification	Undergoes dramatic conformational rearrangements during viral disassembly in the endocytic pathway By similarity.
Sequence similarities	Belongs to the orthoreovirus sigma-1 protein family.
Sequence caution	The sequence AAA47276.1 differs from that shown. Reason: Frameshift at position 410. The sequence AAA66877.1 differs from that shown. Reason: Frameshift at positions 410 and 434.

Ontologies

Keywords
Biological process	Host-virus interaction Viral attachment to host cell Virus entry into host cell
Cellular component	Virion
Domain	Coiled coil
Molecular function	Capsid protein Hemagglutinin
PTM	Glycoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell adhesion Inferred from electronic annotation. Source: InterPro viral attachment to host cell Inferred from electronic annotation. Source: UniProtKB-KW viral entry into host cell Inferred from electronic annotation. Source: UniProtKB-KW viral infectious cycle Inferred from electronic annotation. Source: InterPro
Cellular_component	viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 470

470

Outer capsid protein sigma-1

PRO_0000040667

Regions

Region

1 – 324

324

Tail

Region

325 – 470

146

Head

Coiled coil

26 – 46

21

Potential

Amino acid modifications

Glycosylation

21

1

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

Glycosylation

121

1

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

Glycosylation

205

1

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

Glycosylation

353

1

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

Experimental info

Sequence conflict

91

1

V → G in AAA66877. Ref.1

Sequence conflict

91

1

V → G in AAA47276. Ref.2

Sequence conflict

169

1

S → F in AAA66877. Ref.1

Sequence conflict

384

1

V → L in AAA47276. Ref.2

Sequence conflict

409

1

L → W in AAA47242. Ref.4

Secondary structure

1

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470

Helix Strand Turn

Details...

Beta strand

274 – 278

5

Beta strand

281 – 285

5

Turn

290 – 292

3

Beta strand

293 – 296

4

Beta strand

299 – 304

6

Beta strand

315 – 318

4

Turn

319 – 322

4

Beta strand

323 – 326

4

Helix

328 – 331

4

Beta strand

333 – 345

13

Beta strand

348 – 361

14

Beta strand

364 – 369

6

Beta strand

372 – 375

4

Beta strand

379 – 386

8

Helix

397 – 400

4

Beta strand

409 – 419

11

Beta strand

421 – 437

17

Beta strand

440 – 447

8

Beta strand

454 – 458

5

Beta strand

461 – 466

6

Sequences

	Sequence		Length	Mass (Da)
	P04506 [UniParc]. Last modified November 1, 1990. Version 2. Checksum: F4D18989AD54491C	FASTA	470	51,404
	10 20 30 40 50 60 MDASLITEIR KIVLQLSVSS NGSQSKEIEE IKKQVQVNVD DIRAANIKLD GLGRQIADIS 70 80 90 100 110 120 NSISTIESRL GEMDNRLVGI SSQVTQLSNS VSQNTQSISS LGDRINAVEP RVDSLDTVTS 130 140 150 160 170 180 NLTGRTSTLE ADVGSLRTEL AALTTRVTTE VTRLDGLINS GQNSIGELST RLSNVETSMV 190 200 210 220 230 240 TTAGRGLQKN GNTLNVIVGN GMWFNSSNQL QLDLSGQSKG VGFVGTGMVV KIDTNYFAYN 250 260 270 280 290 300 SNGEITLVSQ INELPSRVST LESAKIDSVL PPLTVREASG VRTLSFGYDT SDFTIINSVL 310 320 330 340 350 360 SLRSRLTLPT YRYPLELDTA NNRVQVADRF GMRTGTWTGQ LQYQHPQLSW RANVTLNLMK 370 380 390 400 410 420 VDDWLVLSFS QMTTNSIMAD GKFVINFVSG LSSGWQTGDT EPSSTIDPLS TTFAAVQFLN 430 440 450 460 470 NGQRIDAFRI MGVSEWTDGE LEIKNYGGTY TGHTQVYWAP WTIMYPCNVR

References

[1]	"Sequences of the S1 genes of the three serotypes of reovirus." Cashdollar L.W., Chmelo R.A., Wiener J.R., Joklik W.K. Proc. Natl. Acad. Sci. U.S.A. 82:24-28(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	"Biosynthesis of reovirus-specified polypeptides. Molecular cDNA cloning and nucleotide sequence of the reovirus serotype 1 Lang strain bicistronic s1 mRNA which encodes the minor capsid polypeptide sigma 1a and the nonstructural polypeptide sigma 1bNS." Munemitsu S.M., Atwater J.A., Samuel C.E. Biochem. Biophys. Res. Commun. 140:508-514(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[3]	"Identification of conserved domains in the cell attachment proteins of the three serotypes of reovirus." Duncan R., Horne D., Cashdollar L.W., Joklik W.K., Lee P.W.K. Virology 174:399-409(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[4]	"Structure of the reovirus cell-attachment protein: a model for the domain organization of sigma 1." Nibert M.L., Dermody T.S., Fields B.N. J. Virol. 64:2976-2989(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[5]	"A plasmid-based reverse genetics system for animal double-stranded RNA viruses." Kobayashi T., Antar A.A., Boehme K.W., Danthi P., Eby E.A., Guglielmi K.M., Holm G.H., Johnson E.M., Maginnis M.S., Naik S., Skelton W.B., Wetzel J.D., Wilson G.J., Chappell J.D., Dermody T.S. Cell Host Microbe 1:147-157(2007) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA]. Strain: Infectious clone.
[6]	"Nature of the 3'-terminal sequences of the plus and minus strands of the S1 gene of reovirus serotypes 1, 2 and 3." Li J.K.-K., Keene J.D., Scheible P.P., Joklik W.K. Virology 105:41-51(1980) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA] OF 1-21.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

HMXRH1. A04122.
HMXRL1. A34829.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4GU3	X-ray	3.60	A/B/C	261-470	[»]
4GU4	X-ray	3.50	A/B/C	261-470	[»]

ProteinModelPortal

P04506.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

2.10.25.20. 1 hit.
2.60.90.20. 1 hit.

InterPro

IPR008982. Adenovirus_pIV-rel_att.
IPR009013. Attachment_protein_shaft_dom.
IPR027314. Sigma1_globular_dom.
IPR002592. Vir_attach_sigma1_reovir.
[Graphical view]

Pfam

PF01664. Reo_sigma1. 1 hit.
[Graphical view]

SUPFAM

SSF49835. Viral_att. 1 hit.

ProtoNet

Search...

Entry information

Entry name

SIGM1_REOVL

Accession

Primary (citable) accession number: P04506
Secondary accession number(s): A4ZY30, P07937

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 13, 1987
Last sequence update:	November 1, 1990
Last modified:	May 1, 2013
This is version 82 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program