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2  structures 75  species 0  interactions 79  sequences 1  architecture

Family: SARS_X4 (PF08779)

Summary: SARS coronavirus X4 like

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This is the Wikipedia entry entitled "SARS coronavirus X4 like protein domain". More...

SARS coronavirus X4 like protein domain Edit Wikipedia article

SARS coronavirus X4 like protein domain
PDB 1xak EBI.jpg
Structure of the SARS-coronavirus orf7a accessory protein
Identifiers
Symbol SARS_X4
Pfam PF08779
InterPro IPR014888

In molecular biology, SARS coronavirus X4 like protein domain is commonly shortened to SARS-X4. This protein domain is only found in viruses. It causes SARS Severe acute respiratory syndrome in humans which causes high rates of death and mortality. It is produced by a type of virus named the coronavirus (SARS-CoV). X4 is the protein domain which is a unique type I transmembrane protein.[1]

Function[edit]

The precise protein of SARS X4 like protein remains to be elucidated however it has been suggested that it has binding activity to integrin I domains.[2] Additionally it is thought to induce apoptosis via a caspase dependent pathway in different types of tissue; or in simpler terms, inducing cell death through an enzymatic pathway.[3] Also, it contains a motif which has been demonstrated to mediate COPII dependent transport out of the endoplasmic reticulum, and the protein is targeted to the Golgi apparatus. It remains unknown as to why the protein may be involved with cell trafficking.[4]

Structure[edit]

The structure of the coronavirus X4 protein (also known as 7a and U122) shows similarities to the immunoglobulin like fold despite the fact they do not share sequence similarity.[2] Their structure contains seven beta strands which form two beta sheets, compactly arranged in an immunoglobulin-like beta sandwich fold.[1]

References[edit]

  1. ^ a b Nelson CA, Pekosz A, Lee CA, Diamond MS, Fremont DH (2005). "Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein.". Structure 13 (1): 75–85. doi:10.1016/j.str.2004.10.010. PMID 15642263. 
  2. ^ a b Hänel K, Stangler T, Stoldt M, Willbold D (May 2006). "Solution structure of the X4 protein coded by the SARS related coronavirus reveals an immunoglobulin like fold and suggests a binding activity to integrin I domains". J. Biomed. Sci. 13 (3): 281–93. doi:10.1007/s11373-005-9043-9. PMID 16328780. 
  3. ^ Satija N, Lal SK (2007). "The molecular biology of SARS coronavirus.". Ann N Y Acad Sci 1102: 26–38. doi:10.1196/annals.1408.002. PMID 17470909. 
  4. ^ Pekosz A, Schaecher SR, Diamond MS, Fremont DH, Sims AC, Baric RS (2006). "Structure, expression, and intracellular localization of the SARS-CoV accessory proteins 7a and 7b.". Adv Exp Med Biol 581: 115–20. doi:10.1007/978-0-387-33012-9_20. PMID 17037516. 

This article incorporates text from the public domain Pfam and InterPro IPR014888

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

SARS coronavirus X4 like Provide feedback

The structure of the coronavirus X4 protein (also known as 7a and U122) shows similarities to the immunoglobulin like fold and suggests a binding activity to integrin I domains [1]. In SARS-CoV- infected cells, the X4 protein is expressed and retained intra-cellularly within the Golgi network [2]. X4 has been implicated to function during the replication cycle of SARS-CoV [3].

Literature references

  1. Hanel K, Stangler T, Stoldt M, Willbold D; , J Biomed Sci. 2005; [Epub ahead of print]: Solution structure of the X4 protein coded by the SARS related coronavirus reveals an immunoglobulin like fold and suggests a binding activity to integrin I domains. PUBMED:16328780 EPMC:16328780

  2. Nelson CA, Pekosz A, Lee CA, Diamond MS, Fremont DH; , Structure. 2005;13:75-85.: Structure and intracellular targeting of the SARS-coronavirus Orf7a accessory protein. PUBMED:15642263 EPMC:15642263

  3. Akerstrom S, Mirazimi A, Tan YJ; , Antiviral Res. 2007;73:219-227.: Inhibition of SARS-CoV replication cycle by small interference RNAs silencing specific SARS proteins, 7a/7b, 3a/3b and S. PUBMED:17112601 EPMC:17112601


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014888

The structure of the coronavirus X4 protein (also known as 7a and U122) shows similarities to the immunoglobulin like fold and suggests a binding activity to integrin I domains [PUBMED:16328780].

Domain organisation

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(18)
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(0)
RP35
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RP55
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RP75
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  Seed
(2)
Full
(79)
Representative proteomes NCBI
(18)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
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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

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Curation and family details

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Seed source: pdb_1yo4
Previous IDs: none
Type: Domain
Author: Mistry J
Number in seed: 2
Number in full: 79
Average length of the domain: 83.90 aa
Average identity of full alignment: 97 %
Average coverage of the sequence by the domain: 68.92 %

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 20.4 20.4
Trusted cut-off 20.6 124.5
Noise cut-off 19.3 15.9
Model length: 84
Family (HMM) version: 5
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Species distribution

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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 SARS_X4 domain has been found. There are 2 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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