Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF THE RAN-BINDING DOMAIN FROM HUMAN RANBP3 (E352A-R353V DOUBLE MUTANT)
 
Authors :  K. Langer, C. Dian, V. Rybin, C. W. Muller, C. Petosa
Date :  06 Feb 11  (Deposition) - 16 Feb 11  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Transport, Crm1-Mediated Nuclear Export (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Langer, C. Dian, V. Rybin, C. W. Muller, C. Petosa
Insights Into The Function Of The Crm1 Cofactor Ranbp3 From The Structure Of Its Ran-Binding Domain
Plos One V. 6 17011 2011
PubMed-ID: 21364925  |  Reference-DOI: 10.1371/JOURNAL.PONE.0017011

(-) Compounds

Molecule 1 - RAN-BINDING PROTEIN 3
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRAN BINDING DOMAIN, RESIDUES 320-454
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsISOFORM3
    SynonymRANBP3-B

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:378 , ARG A:384 , LEU A:385 , HOH A:2138 , HOH A:2139 , HOH A:2140 , HOH A:2141 , HOH A:2142 , ARG B:444BINDING SITE FOR RESIDUE SO4 A1455
2AC2SOFTWARELYS B:403 , SER B:425 , SER B:426 , HOH B:2144BINDING SITE FOR RESIDUE SO4 B1450
3AC3SOFTWAREARG A:359 , ARG A:374 , ARG A:378 , HOH A:2145BINDING SITE FOR RESIDUE SO4 A1456

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y8G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y8G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y8G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y8G)

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 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_HUMAN333-367350--
1.14ENST0000034057814ENSE00001246883chr19:5923314-5923205110RANB3_HUMAN367-403372A:330-335
B:329-335
6
7
1.15bENST0000034057815bENSE00001246878chr19:5921332-5921212121RANB3_HUMAN404-444412A:336-376
B:336-376
41
41
1.16ENST0000034057816ENSE00000666170chr19:5918649-5918507143RANB3_HUMAN444-491482A:376-423 (gaps)
B:376-423 (gaps)
48
48
1.17ENST0000034057817ENSE00000666171chr19:5917991-5917805187RANB3_HUMAN492-554632A:424-454
B:424-449
31
26
1.18aENST0000034057818aENSE00001370280chr19:5917664-59161541511RANB3_HUMAN554-567140--

(-) 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:123
 aligned with RANB3_HUMAN | Q9H6Z4 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:125
                                   407       417       427       437       447       457       467       477       487       497       507       517     
          RANB3_HUMAN   398 ESNVLQMQCKLFVFDKTSQSWVERGRGLLRLNDMASTDDGTLQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRITAMDTEDQGVKVFLISASSKDTGQLYAALHHRILALRSRVEQEQEAK 522
               SCOP domains d2y8ga_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee....eeeeeeeeeeeeeeee......eeeeeeeee.....eeeeee......eeeee..eeeee...--.....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.14  Exon 1.15b  PDB: A:336-376               -----------------------------------------------Exon 1.17  PDB: A:424-454       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.16  PDB: A:376-423 (gaps)                ------------------------------- Transcript 1 (2)
                 2y8g A 330 ESNVLQMQCKLFVFDKTSQSWVAVGRGLLRLNDMASTDDGTLQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRITAMD--DQGVKVFLISASSKDTGQLYAALHHRILALRSRVEQEQEAK 454
                                   339       349       359       369       379       389       399       409 |  |  419       429       439       449     
                                                                                                           411  |                                        
                                                                                                              414                                        

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with RANB3_HUMAN | Q9H6Z4 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:121
                                   406       416       426       436       446       456       466       476       486       496       506       516 
          RANB3_HUMAN   397 AESNVLQMQCKLFVFDKTSQSWVERGRGLLRLNDMASTDDGTLQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRITAMDTEDQGVKVFLISASSKDTGQLYAALHHRILALRSRVEQ 517
               SCOP domains d2y8gb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Ran_BP1-2y8gB01 B:329-437                                                                                    ------------ Pfam domains (1)
           Pfam domains (2) Ran_BP1-2y8gB02 B:329-437                                                                                    ------------ Pfam domains (2)
         Sec.struct. author ..eeeeeeeeeeeeee....eeeeeeeeeeeeeeeee....eeeeeeeeee.....eeeeee......eeeee..eeeeeee..--..eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.14   Exon 1.15b  PDB: B:336-376               -----------------------------------------------Exon 1.17  PDB: B:424-449  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.16  PDB: B:376-423 (gaps)                -------------------------- Transcript 1 (2)
                 2y8g B 329 AESNVLQMQCKLFVFDKTSQSWVAVGRGLLRLNDMASTDDGTLQSRLVMRTQGSLRLILNTKLWAQMQIDKASEKSIRITAMDT--QGVKVFLISASSKDTGQLYAALHHRILALRSRVEQ 449
                                   338       348       358       368       378       388       398       408   |  |418       428       438       448 
                                                                                                             412  |                                  
                                                                                                                415                                  

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y8G)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PH (111)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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

Asymmetric Unit
  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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2y8g)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) 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
  2y8g
    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
  RANB3_HUMAN | Q9H6Z4
    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
  RANB3_HUMAN | Q9H6Z4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RANB3_HUMAN | Q9H6Z42crf 2y8f

(-) Related Entries Specified in the PDB File

2crf SOLUTION STRUCTURE OF THE RAN_BP1 DOMAIN OF RAN- BINDINGPROTEIN-3
2y8f STRUCTURE OF THE RAN-BINDING DOMAIN FROM HUMAN RANBP3 (WILD TYPE)