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

(-) Description

Title :  MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN, NMR, 2 STRUCTURES
 
Authors :  M. Geyer, H. R. Kalbitzer
Date :  12 Apr 99  (Deposition) - 26 May 99  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (2x)
Keywords :  Hiv, Aids, Regulatory Factor, Negative Factor, Nef, Myristoylation, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Geyer, C. E. Munte, J. Schorr, R. Kellner, H. R. Kalbitzer
Structure Of The Anchor-Domain Of Myristoylated And Non-Myristoylated Hiv-1 Nef Protein.
J. Mol. Biol. V. 289 123 1999
PubMed-ID: 10339411  |  Reference-DOI: 10.1006/JMBI.1999.2740
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN (MYRISTATE-GLY2 TO TRP57))
    Chains: A
    Engineered: YES
    Other Details: THIS PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PROTEIN IS FOUND NATURALLY IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1), NL4-3 ISOLATE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (2x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 2)
No.NameCountTypeFull Name
1MYR1Mod. Amino AcidMYRISTIC ACID
2NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (0, 0)

(no "Site" information available for 1QA5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QA5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QA5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QA5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QA5)

(-) Exons   (0, 0)

(no "Exon" information available for 1QA5)

(-) 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:58
 aligned with NEF_HV112 | P04324 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:58
                                    10        20        30        40        50        
             NEF_HV112    1 MGGKWSKSSVVGWPAVRERMRRAEPAADGVGAASRDLEKHGAITSSNTAANNAACAWL 58
               SCOP domains d1qa5a_ A: HIV-1 Nef protein fragments                     SCOP domains
               CATH domains -1qa5A00 A:2-57 HIV 1 nef anchor domain                  - CATH domains
               Pfam domains -F-protein-1qa5A01 A:2-57                                - Pfam domains
         Sec.struct. author ...............hhhhhhh..............hhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                  1qa5 A  1 xGGKWSKSSVVGWPAVRERMRRAEPAADGVGAASRDLEKHGAITSSNTAANNAACAWx 58
                            |       10        20        30        40        50       |
                            |                                                       58-NH2
                            1-MYR
   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
(-)
Class: Peptides (792)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: F-protein] (7)

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (NEF_HV112 | P04324)
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
    MYR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1qa5)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qa5)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1qa5
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NEF_HV112 | P04324
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NEF_HV112 | P04324
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NEF_HV112 | P04324: 1qa4 1zec

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1QA5)