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(-) Description

Title :  SOLUTION STRUCTURE OF THE ARFGAP DOMAIN OF HUMAN RIP
 
Authors :  T. Suetake, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  11 Dec 05  (Deposition) - 11 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rip, Hiv-1, Rev, Arfgap Domain, Zinc Finger, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Suetake, F. Hayashi, S. Yokoyama
Solution Structure Of The Arfgap Domain Of Human Rip
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOPORIN-LIKE PROTEIN RIP
    ChainsA
    EngineeredYES
    Expression System PlasmidP050302-26
    Expression System Vector TypePLASMID
    FragmentARFGAP DOMAIN
    GeneHRB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymHIV-1 REV-BINDING PROTEIN, REV INTERACTING PROTEIN, REV/REX ACTIVATION DOMAIN-BINDING PROTEIN

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:23 , CYS A:26 , CYS A:43 , CYS A:46BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D9L)

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Asn A:54 -Pro A:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D9L)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ARFGAPPS50115 ARF GTPase-activating proteins domain profile.AGFG1_HUMAN11-135  1A:8-128

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003100781bENSE00001855491chr2:228336878-228337304427AGFG1_HUMAN1-56561A:1-50 (gaps)55
1.2ENST000003100782ENSE00001183976chr2:228356263-22835635694AGFG1_HUMAN56-87321A:50-8132
1.5ENST000003100785ENSE00001183971chr2:228384664-228384779116AGFG1_HUMAN88-126391A:82-12039
1.6ENST000003100786ENSE00001183968chr2:228388479-228388641163AGFG1_HUMAN126-180551A:120-134 (gaps)24
1.7bENST000003100787bENSE00001183965chr2:228389478-228389631154AGFG1_HUMAN181-232520--
1.8ENST000003100788ENSE00001183964chr2:228395807-228395926120AGFG1_HUMAN232-272410--
1.10bENST0000031007810bENSE00001183961chr2:228398265-228398474210AGFG1_HUMAN272-342710--
1.11aENST0000031007811aENSE00001183955chr2:228399561-228399741181AGFG1_HUMAN342-402610--
1.12ENST0000031007812ENSE00001183952chr2:228401341-22840142080AGFG1_HUMAN402-429280--
1.13aENST0000031007813aENSE00001183950chr2:228401617-22840170993AGFG1_HUMAN429-460320--
1.15ENST0000031007815ENSE00001183947chr2:228416675-228416833159AGFG1_HUMAN460-513540--
1.16aENST0000031007816aENSE00001183943chr2:228418420-22841851192AGFG1_HUMAN513-543310--
1.17eENST0000031007817eENSE00001882126chr2:228419152-2284213842233AGFG1_HUMAN544-562190--

(-) 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:134
 aligned with AGFG1_HUMAN | P52594 from UniProtKB/Swiss-Prot  Length:562

    Alignment length:148
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141        
          AGFG1_HUMAN     2 AASAKRKQEEKHLKMLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYVPPEQAKVVASVHASISGSSAS 149
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....-----..hhhhhhhhh.................eee.......hhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhh.......hhhhhh---------...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------ARFGAP  PDB: A:8-128 UniProt: 11-135                                                                                         -------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:1-50 (gaps) UniProt: 1-56            -------------------------------Exon 1.5  PDB: A:82-120 UniProt: 88-126----------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.2  PDB: A:50-81          --------------------------------------Exon 1.6 [INCOMPLETE]    Transcript 1 (2)
                 2d9l A   1 GSSG-----SSGLKMLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLRGLNPPHRVKSISMTTFTQQEIEFLQKHGNEVCKQIWLGLFDDRSSAIPDFRDPQKVKEFLQEKYEKKRWYVPPEQAK---------SGPSSG 134
                               |     5        15        25        35        45        55        65        75        85        95       105       115       125  |      -  |     
                               4     5                                                                                                                        128       129     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

(no "SCOP Domain" information available for 2D9L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D9L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D9L)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (AGFG1_HUMAN | P52594)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005096    GTPase activator activity    Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
biological process
    GO:0001675    acrosome assembly    The formation of the acrosome from the spermatid Golgi.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0045109    intermediate filament organization    Control of the spatial distribution of intermediate filaments; includes organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0007289    spermatid nucleus differentiation    The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    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.
cellular component
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AGFG1_HUMAN | P525942olm 2vx8

(-) Related Entries Specified in the PDB File

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