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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF THE TRANS-MEMBRANE DOMAIN OF VPU FROM HIV-1 IN ALIGNED PHOSPHOLIPID BICELLES
 
Authors :  S. H. Park, A. A. De Angelis, A. A. Nevzorov, C. H. Wu, S. J. Opella
Date :  12 Apr 06  (Deposition) - 08 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (21x)
Keywords :  Trans-Membrane Helix, 16C Bicelles, Magnetic Alignment, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Park, A. A. De Angelis, A. A. Nevzorov, C. H. Wu, S. J. Opella
Three-Dimensional Structure Of The Transmembrane Domain Of Vpu From Hiv-1 In Aligned Phospholipid Bicelles.
Biophys. J. V. 91 3032 2006
PubMed-ID: 16861273  |  Reference-DOI: 10.1529/BIOPHYSJ.106.087106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VPU PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET31-B(+)
    Expression System Strain: C43(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: TRANS-MEMBRANE DOMAIN, RESIDUES 2-30
    Gene: VPU
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synonym: U ORF PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (21x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2GOH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GOH)

(-) 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:19
 aligned with Q2NN19_9HIV1 | Q2NN19 from UniProtKB/TrEMBL  Length:80

    Alignment length:19
                                    16         
          Q2NN19_9HIV1    7 AIVALVVAIIIAIVVWSIV 25
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                  2goh A  7 AIVALVVAIIIAIVVWSIV 25
                                    16         


Chain A from PDB  Type:PROTEIN  Length:19
 aligned with VPU_HV1LW | Q70625 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:19
                                    16         
             VPU_HV1LW    7 AIVALVVAIIIAIVVWSIV 25
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                  2goh A  7 AIVALVVAIIIAIVVWSIV 25
                                    16
   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  (0, 0)

(no "SCOP Domain" information available for 2GOH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 23)

NMR Structure(hide GO term definitions)
Chain A   (VPU_HV1LW | Q70625)
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.

Chain A   (Q2NN19_9HIV1 | Q2NN19)
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: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: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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  VPU_HV1LW | Q70625
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 Related Entries

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

UniProtKB/Swiss-Prot
        VPU_HV1LW | Q70625: 1pi7 1pi8 1pje 2gof

(-) Related Entries Specified in the PDB File

2gof THREE-DIMENSIONAL STRUCTURE OF THE TRANS-MEMBRANE DOMAIN OF VPU FROM HIV-1 IN ALIGNED PHOSPHOLIPID BICELLES