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(-) Description

Title :  SOLUTION STRUCTURE OF THE SARS-CORONAVIRUS HR2 DOMAIN
 
Authors :  M. Caffrey, S. Hakansson-Mcreynolds, S. Jiang
Date :  06 Feb 06  (Deposition) - 07 Mar 06  (Release) - 20 May 08  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C
Keywords :  Prefusion Intermediate, Trimer, Coiled-Coil, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hakansson-Mcreynolds, S. Jiang, L. Rong, M. Caffrey
Solution Structure Of The Severe Acute Respiratory Syndrome-Coronavirus Heptad Repeat 2 Domain In The Prefusion State
J. Biol. Chem. V. 281 11965 2006
PubMed-ID: 16507566  |  Reference-DOI: 10.1074/JBC.M601174200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SPIKE GLYCOPROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: HR2 DOMAIN, RESIDUES 1140-1193
    Gene: S
    Organism Scientific: SARS CORONAVIRUS
    Organism Taxid: 227859

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2FXP)

(-) Sites  (0, 0)

(no "Site" information available for 2FXP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FXP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FXP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 6)

NMR Structure (2, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SPIKE_CVHSA_042 *L1148FSPIKE_CVHSA  ---  ---A/B/CL10F
2UniProtVAR_SPIKE_CVHSA_043 *K1163ESPIKE_CVHSA  ---  ---A/B/CK25E
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FXP)

(-) Exons   (0, 0)

(no "Exon" information available for 2FXP)

(-) Sequences/Alignments

NMR Structure
   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:55
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:55
                                  1148      1158      1168      1178      1188     
         SPIKE_CVHSA   1139 KNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK 1193
               SCOP domains -d2fxpa1 A:2-55 E2 spike glycoprotein                   SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------F--------------E------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                2fxp A    1 GSHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK   55
                                    10        20        30        40        50     


Chain B from PDB  Type:PROTEIN  Length:55
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:55
                                  1148      1158      1168      1178      1188     
         SPIKE_CVHSA   1139 KNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK 1193
               SCOP domains d2fxpb_ B: E2 spike glycoprotein                        SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------F--------------E------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                2fxp B    1 GSHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK   55
                                    10        20        30        40        50     


Chain C from PDB  Type:PROTEIN  Length:55
 aligned with SPIKE_CVHSA | P59594 from UniProtKB/Swiss-Prot  Length:1255

    Alignment length:55
                                  1148      1158      1168      1178      1188     
         SPIKE_CVHSA   1139 KNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK 1193
               SCOP domains d2fxpc_ C: E2 spike glycoprotein                        SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------F--------------E------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                2fxp C    1 GSHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK   55
                                    10        20        30        40        50
   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, 3)

NMR Structure
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2FXP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FXP)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A,B,C   (SPIKE_CVHSA | P59594)
molecular function
    GO:0046789    host cell surface receptor binding    Interacting selectively and non-covalently with a receptor on the host cell surface.
biological process
    GO:0039654    fusion of virus membrane with host endosome membrane    Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0046813    receptor-mediated virion attachment to host cell    The process by which a virion attaches to a host cell by binding to a receptor on the host cell surface.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    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.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    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:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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  2fxp
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 Related Entries

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

UniProtKB/Swiss-Prot
        SPIKE_CVHSA | P59594: 1q4z 1t7g 1u4k 1wnc 1wyy 1xjp 1zv7 1zv8 1zva 1zvb 2ajf 2beq 2bez 2dd8 2ghv 2ghw 2rum 2run 2ruo 3bgf 3d0g 3d0h 3d0i 3sci 3scj 3sck 3scl 5wrg 5x4s 5xlr

(-) Related Entries Specified in the PDB File

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