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 :  SOLUTION STRUCTURE OF THE RAN_BP1 DOMAIN OF RAN-BINDING PROTEIN-3
 
Authors :  H. P. Zhang, T. Nagashima, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 May 05  (Deposition) - 20 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Ran_bp1 Domain, Ran-Binding Protein 3, Ranbp3, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. Zhang, T. Nagashima, F. Hayashi, S. Yokoyama
Solution Structure Of The Ran_bp1 Domain Of Ran-Binding Protein-3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAN BINDING PROTEIN 3
    Chains: A
    Engineered: YES
    Expression System Plasmid: P041004-03
    Expression System Vector Type: PLASMID
    Fragment: RAN_BP1 DOMAIN
    Gene: RANBP3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2CRF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RANBD1PS50196 Ran binding domain type 1 profile.RANB3_HUMAN385-466  1A:13-94

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003405781ENSE00001428577chr19:5978320-5978072249RANB3_HUMAN1-880--
1.3bENST000003405783bENSE00001115985chr19:5957984-595792956RANB3_HUMAN8-26190--
1.4ENST000003405784ENSE00001115983chr19:5951607-5951404204RANB3_HUMAN27-94680--
1.5ENST000003405785ENSE00001306174chr19:5941846-594181037RANB3_HUMAN95-107130--
1.6ENST000003405786ENSE00000666160chr19:5941718-594163287RANB3_HUMAN107-136300--
1.7ENST000003405787ENSE00000666161chr19:5933490-593342566RANB3_HUMAN136-158230--
1.8ENST000003405788ENSE00000666162chr19:5932555-593246393RANB3_HUMAN158-189320--
1.9bENST000003405789bENSE00000666163chr19:5931542-5931415128RANB3_HUMAN189-231430--
1.10ENST0000034057810ENSE00001246903chr19:5928098-5927979120RANB3_HUMAN232-271400--
1.11ENST0000034057811ENSE00001246896chr19:5925748-5925645104RANB3_HUMAN272-306350--
1.12ENST0000034057812ENSE00000666166chr19:5924916-592483879RANB3_HUMAN306-332270--
1.13ENST0000034057813ENSE00001246887chr19:5923925-5923823103RANB3_HUMAN333-367351A:1-66
1.14ENST0000034057814ENSE00001246883chr19:5923314-5923205110RANB3_HUMAN367-403371A:7-3125
1.15bENST0000034057815bENSE00001246878chr19:5921332-5921212121RANB3_HUMAN404-444411A:32-7241
1.16ENST0000034057816ENSE00000666170chr19:5918649-5918507143RANB3_HUMAN444-491481A:72-11948
1.17ENST0000034057817ENSE00000666171chr19:5917991-5917805187RANB3_HUMAN492-554631A:120-150 (gaps)58
1.18aENST0000034057818aENSE00001370280chr19:5917664-59161541511RANB3_HUMAN554-567140--

(-) 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:150
 aligned with RANB3_HUMAN | Q9H6Z4 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:196
                                   363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543      
          RANB3_HUMAN   354 GSESSSQEATPEKESLAESAAAYTKATARKCLLEKVEVITGEEAESNVLQMQCKLFVFDKTSQSWVERGRGLLRLNDMASTDDGTLQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRITAMDTEDQGVKVFLISASSKDTGQLYAALHHRILALRSRVEQEQEAKMPAPEPGAAPSNEEDDSDDDDVLAPSG 549
               SCOP domains --------------------------d2crfa1 A:8-144 Ran binding protein 3                                                                                                    --------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-------------------....................eeeeeeeeeeeeee....eeeeeeeeeeeeeeee......eeeeeeeee.....eeeeee.............eeeeeee......eeeeeee....hhhhhhhhhhhhhhhhhhhh.-------------....--------------.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------RANBD1  PDB: A:13-94 UniProt: 385-466                                             ----------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.13     ------------------------------------Exon 1.15b  PDB: A:32-72 UniProt: 404-444-----------------------------------------------Exon 1.17  PDB: A:120-150 (gaps) UniProt: 492-554          Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.14  PDB: A:7-31 [INCOMPLETE]  ----------------------------------------Exon 1.16  PDB: A:72-119 UniProt: 444-491       ---------------------------------------------------------- Transcript 1 (2)
                 2crf A   1 GSSGSS-------------------GTARKCLLEKVEVITGEEAESNVLQMQCKLFVFDKTSQSWVERGRGLLRLNDMASTDDGTLQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIHITAMDTEDQGVKVFLISASSKDTGQLYAALHHRILALRSRVE-------------SGPS--------------SG 150
                                 |   -         -     |  11        21        31        41        51        61        71        81        91       101       111       121       131       141  |      -      |148         -    | 
                                 6                   7                                                                                                                                      144           145  |            149 
                                                                                                                                                                                                             148
   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: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (RANB3_HUMAN | Q9H6Z4)
molecular function
    GO:0070412    R-SMAD binding    Interacting selectively and non-covalently with a receptor-regulated SMAD signaling protein.
    GO:0008536    Ran GTPase binding    Interacting selectively and non-covalently with Ran, a conserved Ras-like GTP-binding protein, implicated in nucleocytoplasmic transport, cell cycle progression, spindle assembly, nuclear organization and nuclear envelope (NE) assembly.
    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:0046907    intracellular transport    The directed movement of substances within a cell.
    GO:0046827    positive regulation of protein export from nucleus    Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

 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 2crf)
 
  Sites
(no "Sites" information available for 2crf)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2crf)
 

(-) 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
  2crf
    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
  RANB3_HUMAN | Q9H6Z4
    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
  RANB3_HUMAN | Q9H6Z4
    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
        RANB3_HUMAN | Q9H6Z4: 2y8f 2y8g

(-) Related Entries Specified in the PDB File

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