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(-) Description

Title :  CORE STRUCTURE OF GP2 FROM EBOLA VIRUS
 
Authors :  V. N. Malashkevich, B. J. Schneider, M. L. Mcnally, M. A. Milhollen, J. X. Pang, P. S. Kim
Date :  24 Dec 98  (Deposition) - 18 May 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Envelope Glycoprotein, Filovirus, Ebola Virus, Gp2, Coat Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. N. Malashkevich, B. J. Schneider, M. L. Mcnally, M. A. Milhollen, J. X. Pang, P. S. Kim
Core Structure Of The Envelope Glycoprotein Gp2 From Ebola Virus At 1. 9-A Resolution.
Proc. Natl. Acad. Sci. Usa V. 96 2662 1999
PubMed-ID: 10077567  |  Reference-DOI: 10.1073/PNAS.96.6.2662
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EBOLA VIRUS ENVELOPE GLYCOPROTEIN
    Cellular LocationVIRAL MEMBRANE
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System GeneGP41
    Expression System PlasmidPMMHB
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentPROTEASE-RESISTANT FRAGMENT
    GeneGP41
    MutationYES
    Organism ScientificZAIRE EBOLAVIRUS - MAYINGA (ZAIRE, 1976)
    Organism Taxid128952
    StrainZAIRE MAYINGA
    VariantZAIRE ISOLATE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:583 , ASN A:586 , SER B:583 , ASN B:586 , ASN C:586BINDING SITE FOR RESIDUE CL A 1
2CLUNKNOWNASN A:586 , ASN B:586 , ASN C:586CHLORIDE-BINDING SITE

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:601 -A:608
2B:601 -B:608
3C:601 -C:608

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EBO)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2EBO)

(-) 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:74
 aligned with VGP_EBOZM | Q05320 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:74
                                   566       576       586       596       606       616       626    
            VGP_EBOZM   557 GLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDF 630
               SCOP domains d2eboa_ A: Core structure of Ebo gp2                                       SCOP domains
               CATH domains 2eboA00 A:557-630  [code=1.10.287.210, no name defined]                    CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2ebo A 557 GLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCAIEPHDWTKNITDKIDQIIHDF 630
                                   566       576       586       596       606       616       626    

Chain B from PDB  Type:PROTEIN  Length:74
 aligned with VGP_EBOZM | Q05320 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:74
                                   566       576       586       596       606       616       626    
            VGP_EBOZM   557 GLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDF 630
               SCOP domains d2ebob_ B: Core structure of Ebo gp2                                       SCOP domains
               CATH domains 2eboB00 B:557-630  [code=1.10.287.210, no name defined]                    CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh..hhhhh...........hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2ebo B 557 GLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCAIEPHDWTKNITDKIDQIIHDF 630
                                   566       576       586       596       606       616       626    

Chain C from PDB  Type:PROTEIN  Length:74
 aligned with VGP_EBOZM | Q05320 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:74
                                   566       576       586       596       606       616       626    
            VGP_EBOZM   557 GLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDF 630
               SCOP domains d2eboc_ C: Core structure of Ebo gp2                                       SCOP domains
               CATH domains 2eboC00 C:557-630  [code=1.10.287.210, no name defined]                    CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2ebo C 557 GLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCAIEPHDWTKNITDKIDQIIHDF 630
                                   566       576       586       596       606       616       626    

   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)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (VGP_EBOZM | Q05320)
biological process
    GO:0075512    clathrin-dependent endocytosis of virus by host cell    Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
    GO:0075509    endocytosis involved in viral entry into host cell    Any endocytosis that is involved in the uptake of a virus into a host cell.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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: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:0039503    suppression by virus of host innate immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
    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:0039502    suppression by virus of host type I interferon-mediated signaling pathway    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0046761    viral budding from plasma membrane    A viral budding that starts with formation of a membrane curvature in the host plasma membrane.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.
    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: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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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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        VGP_EBOZM | Q053202rlj 3csy 5fhc 5hj3 5jq3 5jq7 5jqb 5kel 5kem 5ken

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