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(-) Description

Title :  VISNA TM CORE STRUCTURE
 
Authors :  V. N. Malashkevich, M. Singh, P. S. Kim
Date :  18 Jun 01  (Deposition) - 25 Jul 01  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Envelope Glycoprotein, Retrovirus, Hiv, Siv, Gp41, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, M. Singh, P. S. Kim
The Trimer-Of-Hairpins Motif In Membrane Fusion: Visna Virus.
Proc. Natl. Acad. Sci. Usa V. 98 8502 2001
PubMed-ID: 11447278  |  Reference-DOI: 10.1073/PNAS.151254798
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENV POLYPROTEIN
    Chains: A
    Engineered: YES
    Other Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN VISNA VIRUS.
    Synonym: COAT POLYPROTEIN
    Synthetic: YES
 
Molecule 2 - ENV POLYPROTEIN
    Chains: B
    Engineered: YES
    Other Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN VISNA VIRUS.
    Synonym: COAT POLYPROTEIN
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2NH22Mod. Amino AcidAMINO GROUP
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1ACE6Mod. Amino AcidACETYL GROUP
2NH26Mod. Amino AcidAMINO GROUP

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:549 , HOH B:66BINDING SITE FOR RESIDUE ACE A 545
2AC2SOFTWAREGLN B:629 , TRP B:631 , HOH B:47BINDING SITE FOR RESIDUE ACE B 627
3AC3SOFTWAREALA A:585 , HOH B:12BINDING SITE FOR RESIDUE NH2 A 586
4AC4SOFTWAREALA B:660 , ARG B:661BINDING SITE FOR RESIDUE NH2 B 662

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JEK)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JEK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1JEK)

(-) Sequences/Alignments

Asymmetric 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:42
 aligned with ENV_VILVK | P35954 from UniProtKB/Swiss-Prot  Length:983

    Alignment length:42
                                   701       711       721       731  
            ENV_VILVK   692 VQSLANATAAQQEVLEASYAMVQHIAKGIRILEARVARVEAL 733
               SCOP domains d1jek.1 A:,B:                              SCOP domains
               CATH domains -1jekA00 A:546-585                       - CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
                 Transcript ------------------------------------------ Transcript
                 1jek A 545 xQSLANATAAQQEVLEASYAMVQHIAKGIRILEARVARVEAx 586
                            |      554       564       574       584 |
                            |                                      586-NH2
                          545-ACE                                     


Chain B from PDB  Type:PROTEIN  Length:36
 aligned with ENV_VILVK | P35954 from UniProtKB/Swiss-Prot  Length:983

    Alignment length:36
                                   783       793       803      
            ENV_VILVK   774 TWQQWEEEIEQHEGNLSLLLREAALQVHIAQRDARR 809
               SCOP domains d1jek.1 A:,B:                        SCOP domains
               CATH domains ------------------------------------ CATH domains
           Pfam domains (1) -GP41-1jekB01 B:628-661            - Pfam domains (1)
           Pfam domains (2) -GP41-1jekB02 B:628-661            - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------ PROSITE
                 Transcript ------------------------------------ Transcript
                 1jek B 627 xWQQWEEEIEQHEGNLSLLLREAALQVHIAQRDARx 662
                            |      636       646       656     |
                            |                                662-NH2
                          627-ACE
   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 Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: GP41] (22)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ENV_VILVK | P35954)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    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: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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  1jek
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