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(-) Description

Title :  STRUCTURE OF THE SARS-CORONAVIRUS ORF7A ACCESSORY PROTEIN
 
Authors :  C. A. Nelson, C. A. Lee, D. H. Fremont, Midwest Center For Structural Genomics (Mcsg)
Date :  26 Aug 04  (Deposition) - 05 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  I-Set Ig Domain, Beta Sandwich, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Nelson, A. Pekosz, C. A. Lee, M. S. Diamond, D. H. Fremont
Structure And Intracellular Targeting Of The Sars-Coronavirus Orf7A Accessory Protein.
Structure V. 13 75 2005
PubMed-ID: 15642263  |  Reference-DOI: 10.1016/J.STR.2004.10.010
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SARS ORF7A ACCESSORY PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21A (EMD BIOSCIENCES)
    Expression System Strain: BL21(DE3)RIL CODON (+) E.COLI CELLS (STRATAGENE)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL ECTODOMAIN (RESIDUES 14-96)
    Organism Scientific: SARS CORONAVIRUS
    Organism Taxid: 227859

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XAK)

(-) Sites  (0, 0)

(no "Site" information available for 1XAK)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:8 -A:43
2A:20 -A:52

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XAK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_NS7A_CVHSA_001 *G38ANS7A_CVHSA  ---  ---AG23A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XAK)

(-) Exons   (0, 0)

(no "Exon" information available for 1XAK)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:68
 aligned with NS7A_CVHSA | P59635 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:68
                                    24        34        44        54        64        74        
            NS7A_CVHSA   15 CELYHYQECVRGTTVLLKEPCPSGTYEGNSPFHPLADNKFALTCTSTHFAFACADGTRHTYQLRARSV 82
               SCOP domains d1xaka_ A: Accessory protein X4 (ORF8, ORF7a)                        SCOP domains
               CATH domains 1xakA00 A:-1-67 Sars orf7a accessory protein.                        CATH domains
               Pfam domains -SARS_X4-1xakA01 A:1-67                                              Pfam domains
         Sec.struct. author .eeeeeeeee...eeeee......eeee.....ee...eeeee...eeeeee.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -----------------------A-------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                  1xak A -1 CELYHYQECVRGTTVILKEPCPSGTYEGNSPFHPLADNKFALTCTSTHFAFACADGTRHTYQLRARSV 67
                            ||       9        19        29        39        49        59        
                            ||                                                                  
                           -1|                                                                  
                             1
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SARS_X4] (2)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NS7A_CVHSA | P59635)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0039646    modulation by virus of host G0/G1 transition checkpoint    Any viral process that modulates the frequency, rate or extent of the host cell G0/G1 transition checkpoint.
    GO:0060153    modulation by virus of host cell cycle    Any viral process that modulates the rate or extent of progression through the cell cycle.
    GO:0039587    suppression by virus of host tetherin activity    Any process in which a virus stops, prevents, or reduces the activity of host tetherin activity. Tetherin (also known as BST2) is an alpha interferon-inducible cellular factor that impairs the release of many enveloped viruses. By blocking tetherin activity, many viruses circumvent its antiviral effects.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0044177    host cell Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic host cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack.
    GO:0044178    host cell Golgi membrane    The lipid bilayer surrounding any of the compartments of the host cell Golgi apparatus.
    GO:0044165    host cell endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0044167    host cell endoplasmic reticulum membrane    The lipid bilayer surrounding the host cell endoplasmic reticulum.
    GO:0044173    host cell endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the host cell ER-Golgi intermediate compartment system.
    GO:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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  NS7A_CVHSA | P59635
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NS7A_CVHSA | P59635: 1yo4

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