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(-) Description

Title :  NMR SOLUTION STRUCTURE OF THE HIV-1 VPU CYTOPLASMIC DOMAIN, 9 STRUCTURES
 
Authors :  D. Willbold, S. Hoffmann, P. Rosch
Date :  28 Jan 97  (Deposition) - 15 May 97  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (9x)
Keywords :  Hiv, Vpu, Aids (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Willbold, S. Hoffmann, P. Rosch
Secondary Structure And Tertiary Fold Of The Human Immunodeficiency Virus Protein U (Vpu) Cytoplasmic Domain In Solution.
Eur. J. Biochem. V. 245 581 1997
PubMed-ID: 9182993  |  Reference-DOI: 10.1111/J.1432-1033.1997.T01-1-00581.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VPU PROTEIN
    Cell Line: BL21
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B (NOVAGEN)
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET16B (NOVAGEN)
    Expression System Vector Type: PLASMID
    Fragment: CYTOPLASMIC DOMAIN RESIDUES 39 - 81
    Gene: SYNTHETIC GENE
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Strain: SF162 ISOLATE
    Synonym: VPU(39-81)

 Structural Features

(-) Chains, Units

  
NMR Structure (9x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1VPU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VPU)

(-) 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:45
 aligned with VPU_HV1S1 | P19554 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:45
                                    46        56        66        76     
             VPU_HV1S1   37 RKIDRLIDRITERAEDSGNESEGDQEELSALVERGHLAPWDVDDL 81
               SCOP domains d1vpua_ A: HIV-1 VPU cytoplasmic domain       SCOP domains
               CATH domains 1vpuA00 A:37-81                               CATH domains
               Pfam domains --Vpu-1vpuA01 A:39-80                       - Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.........hhhh...........hhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------- PROSITE
                 Transcript --------------------------------------------- Transcript
                  1vpu A 37 LQIDRLIDRITERAEDSGNESEGDQEELSALVERGHLAPWDVDDL 81
                                    46        56        66        76
   Legend:   → Mismatch (orange background)
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  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)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Vpu] (4)

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (VPU_HV1S1 | P19554)
molecular function
    GO:0042609    CD4 receptor binding    Interacting selectively and non-covalently with a CD4, a receptor found on the surface of T cells, monocytes and macrophages.
    GO:0005261    cation channel activity    Enables the energy-independent passage of cations across a lipid bilayer down a concentration gradient.
biological process
    GO:0098655    cation transmembrane transport    A process in which a cation is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    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:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0032801    receptor catabolic process    The chemical reactions and pathways resulting in the breakdown of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    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:0019076    viral release from host cell    The dissemination of mature viral particles from the host cell, e.g. by cell lysis or the budding of virus particles from the cell membrane.
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: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.

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 Related Entries

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UniProtKB/Swiss-Prot
        VPU_HV1S1 | P19554: 2k7y 4p6z

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