Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  HIV-1 NEF (REGULATORY FACTOR), NMR, 40 STRUCTURES
 
Authors :  S. Grzesiek, A. Bax, G. M. Clore, A. M. Gronenborn, J. S. Hu, J. Kaufman, I S. J. Stahl, N. Tjandra, P. T. Wingfield
Date :  12 Feb 97  (Deposition) - 07 Jul 97  (Release) - 13 Jul 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (40x)
NMR Structure *:  A  (1x)
Keywords :  Regulatory Factor, Aids, Myristylation, Gtp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Grzesiek, A. Bax, J. S. Hu, J. Kaufman, I. Palmer, S. J. Stahl, N. Tjandra, P. T. Wingfield
Refined Solution Structure And Backbone Dynamics Of Hiv-1 Nef.
Protein Sci. V. 6 1248 1997
PubMed-ID: 9194185
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEGATIVE FACTOR (F-PROTEIN)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System GeneHIV-1 NEF
    Expression System PlasmidPET11A
    Expression System StrainDE3
    Expression System Taxid562
    GeneHIV-1 NEF
    MutationYES
    Organism ScientificHUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid11678
    StrainBH10
    SynonymHIV-1 NEF

 Structural Features

(-) Chains, Units

  1
NMR Structure (40x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2NEF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NEF)

(-) 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:136
 aligned with NEF_HV1LW | Q70627 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:151
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205 
            NEF_HV1LW    56 AWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGIRYPLTFGWCYKLVPVEPEKLEEANKGENTSLLHPVSLHGMDDPEREVLEWRFDSRLAFHHVARELHPEYFKNC 206
               SCOP domains d2nefa_ A: Regulatory factor Nef                                                                                                                        SCOP domains
               CATH domains 2nefA00 A:56-206 Nef Regulatory Factor                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhh..hhhhhhhhhhhhhh.....eee..hhhhhhhhhh...........eee....eeeee.....eeeee...........---------------.......eeeeeehhhh...hhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nef A  56 AWLEAQEEEEVGFPVTPQVPLRPMTYKAAVDLSHFLKEKGGLEGLIHSQRRQDILDLWIYHTQGYFPDWQNYTPGPGIRYPLTFGWCYKLVPVEPEKLEEANK---------------DDPEREVLEWRFDSRLAFHHMARELHPEYFKNA 206
                                    65        75        85        95       105       115       125       135       145       155  |      -       175       185       195       205 
                                                                                                                                158             174                                

   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)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (NEF_HV1LW | Q70627)
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: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: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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2nef)
 
  Sites
(no "Sites" information available for 2nef)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2nef)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2nef
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NEF_HV1LW | Q70627
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  NEF_HV1LW | Q70627
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2NEF)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2NEF)