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18  structures 42  species 2  interactions 120  sequences 1  architecture

Family: Sigma_1_2 (PF03084)

Summary: Reoviral Sigma1/Sigma2 family

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Reoviral Sigma1/Sigma2 family Provide feedback

Reoviruses are double-stranded RNA viruses. They lack a membrane envelope and their capsid is organised in two concentric icosahedral layers: an inner core and an outer capsid layer. The sigma1 protein is found in the outer capsid, and the sigma2 protein is found in the core. There are four other kinds of protein (besides sigma2) in the core, termed lambda 1-3, mu2. Interactions between sigma2 and lambda 1 and lambda 3 are thought to initiate core formation, followed by mu2 and lambda2 [5]. Sigma1 is a trimeric protein, and is positioned at the 12 vertices of the icosahedral outer capsid layer. Its N-terminal fibrous tail, arranged as a triple coiled coil, anchors it in the virion, and a C-terminal globular head interacts with the cellular receptor [2]. These two parts form by separate trimerisation events. The N-terminal fibrous tail forms on the polysome, without the involvement of ATP or chaperones. The post- translational assembly of the C-terminal globular head involves the chaperone activity of Hsp90, which is associated with phosphorylation of Hsp90 during the process [2]. Sigma1 protein acts as a cell attachment protein, and determines viral virulence, pathways of spread, and tropism. Junctional adhesion molecule has been identified as a receptor for sigma1 [1]. In type 3 reoviruses, a small region, predicted to form a beta sheet, in the N-terminal tail was found to bind target cell surface sialic acid (i.e. sialic acid acts as a co-receptor) and promote apoptosis [4]. The sigma1 protein also binds to the lambda2 core protein [3].

Literature references

  1. Barton ES, Forrest JC, Connolly JL, Chappell JD, Liu Y, Schnell FJ, Nusrat A, Parkos CA, Dermody TS; , Cell 2001;104:441-451.: Junction adhesion molecule is a receptor for reovirus. PUBMED:11239401 EPMC:11239401

  2. Zhao YG, Gilmore R, Leone G, Coffey MC, Weber B, Lee PW; , J Biol Chem 2001;0:0-0.: Hsp90 phosphorylation is linked to its chaperoning function: Assembly of the reovirus cell attachment protein. PUBMED:11438552 EPMC:11438552

  3. Luongo CL, Dryden KA, Farsetta DL, Margraf RL, Severson TF, Olson NH, Fields BN, Baker TS, Nibert ML; , J Virol 1997;71:8035-8040.: Localization of a C-terminal region of lambda2 protein in reovirus cores. PUBMED:9311901 EPMC:9311901

  4. Connolly JL, Barton ES, Dermody TS; , J Virol 2001;75:4029-4039.: Reovirus binding to cell surface sialic acid potentiates virus-induced apoptosis. PUBMED:11287552 EPMC:11287552

  5. Hazelton PR, Coombs KM; , J Virol 1999;73:2298-2308.: The reovirus mutant tsA279 L2 gene is associated with generation of a spikeless core particle: implications for capsid assembly. PUBMED:9971813 EPMC:9971813


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004317

Reoviruses are double-stranded RNA viruses that lack a membrane envelope. Their capsid is organised in two concentric icosahedral layers: an inner core and an outer capsid layer. The sigma1 protein is found in the outer capsid, and the sigma2 protein is found in the core. There are four other kinds of protein (besides sigma2) in the core, termed lambda 1-3, mu2. Interactions between sigma2 and lambda 1 and lambda 3 are thought to initiate core formation, followed by mu2 and lambda2 [PUBMED:9971813].

Sigma1 is a trimeric protein, and is positioned at the 12 vertices of the icosahedral outer capsid layer. Its N-terminal fibrous tail, arranged as a triple coiled coil, anchors it in the virion, and a C-terminal globular head interacts with the cellular receptor [PUBMED:11438552]. These two parts form by separate trimerization events. The N-terminal fibrous tail forms on the polysome, without the involvement of ATP or chaperones. The post- translational assembly of the C-terminal globular head involves the chaperone activity of Hsp90, which is associated with phosphorylation of Hsp90 during the process [PUBMED:11438552]. Sigma1 protein acts as a cell attachment protein, and determines viral virulence, pathways of spread, and tropism. Junctional adhesion molecule has been identified as a receptor for sigma1 [PUBMED:11239401]. In type 3 reoviruses, a small region, predicted to form a beta sheet, in the N-terminal tail was found to bind target cell surface sialic acid (i.e. sialic acid acts as a co-receptor) and promote apoptosis [PUBMED:11287552]. The sigma1 protein also binds to the lambda2 core protein [PUBMED:9311901].

Domain organisation

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Alignments

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(98)
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  Seed
(4)
Full
(120)
Representative proteomes NCBI
(98)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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  Seed
(4)
Full
(120)
Representative proteomes NCBI
(98)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1759 (release 6.4)
Previous IDs: none
Type: Family
Author: Mifsud W
Number in seed: 4
Number in full: 120
Average length of the domain: 322.90 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 99.77 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 26.3 64.1
Noise cut-off 16.9 16.5
Model length: 415
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Reovirus_M2 Reovirus_L2

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Sigma_1_2 domain has been found. There are 18 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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