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(-) Description

Title :  HIV-1 NEF PROTEIN, UNLIGANDED CORE DOMAIN
 
Authors :  S. Arold, P. Franken, C. Dumas
Date :  21 Sep 97  (Deposition) - 25 Mar 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Myristylation, Gtp-Binding, Phosphorylation, Hiv-1, Nef, Virus, Pxxp Motif (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Arold, P. Franken, M. P. Strub, F. Hoh, S. Benichou, R. Benarous, C. Dumas
The Crystal Structure Of Hiv-1 Nef Protein Bound To The Fyn Kinase Sh3 Domain Suggests A Role For This Complex In Altered T Cell Receptor Signaling.
Structure V. 5 1361 1997
PubMed-ID: 9351809  |  Reference-DOI: 10.1016/S0969-2126(97)00286-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEGATIVE FACTOR
    Cell LineBL21
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System GeneHIV-1 NEF
    Expression System PlasmidPGEX-2T
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    FragmentCORE DOMAIN
    GeneHIV-1 NEF
    MutationYES
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid11676
    SynonymNEF, F-PROTEIN
    VariantISOLATE LAI

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1AVV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:130 -Pro A:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1AVV)

(-) 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:99
 aligned with NEF_HV1BR | P03406 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:130
                                    83        93       103       113       123       133       143       153       163       173       183       193       203
            NEF_HV1BR    74 VPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVPVEPDKVEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYF 203
               SCOP domains d1avva_ A: Regulatory factor Nef                                                                                                   SCOP domains
               CATH domains 1avvA00 A:74-203 Nef Regulatory Factor                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh..........hhhhhhhhhhhhhhh........................eeee.-------------------------------...eeee.hhhh...hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1avv A  74 VPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGVRYPLTFGWCYKLVP-------------------------------EVLEWRFDSRLAFHHVARELHPEYF 203
                                    83        93       103       113       123       133       143   |     -         -         -     | 183       193       203
                                                                                                   147                             179                        

   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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AVV)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A   (NEF_HV1BR | P03406)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    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:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0042288    MHC class I protein binding    Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0031996    thioesterase binding    Interacting selectively and non-covalently with any thioesterase enzyme.
biological process
    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:0052085    negative regulation by symbiont of host T-cell mediated immune response    Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of the T-cell mediated immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0045225    negative regulation of CD4 biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4.
    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:0043946    positive regulation of catalytic activity in other organism involved in symbiotic interaction    Any process in which an organism activates, maintains or increases the frequency, rate or extent of enzyme activity in a second organism, where the two organisms are in a symbiotic interaction.
    GO:0050863    regulation of T cell activation    Any process that modulates the frequency, rate or extent of T cell activation.
    GO:0050848    regulation of calcium-mediated signaling    Any process that modulates the frequency, rate or extent of calcium-mediated signaling, the process in which a cell uses calcium ions to convert an extracellular signal into a response.
    GO:0039504    suppression by virus of host adaptive immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the adaptive immune response of the host organism, an immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).
    GO:0046776    suppression by virus of host antigen processing and presentation of peptide antigen via MHC class I    Any viral process that inhibits a host antigen-presenting cell expressing a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
    GO:0039505    suppression by virus of host antigen processing and presentation of peptide antigen via MHC class II    Any viral process that inhibits a host antigen-presenting cell expressing a peptide antigen on its cell surface in association with an MHC class II protein complex.
    GO:0039521    suppression by virus of host autophagy    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of autophagy in the host.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    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.
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:0044177    host cell Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic host cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack.
    GO:0044178    host cell Golgi membrane    The lipid bilayer surrounding any of the compartments of the host cell Golgi apparatus.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEF_HV1BR | P034061avz 1efn 4d8d

(-) Related Entries Specified in the PDB File

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