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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE MPPN DOMAIN OF MOUSE NUP35
 
Authors :  N. Handa, K. Murayama, M. Kukimoto, H. Hamana, T. Uchikubo, C. Takemoto, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  05 Jan 05  (Deposition) - 05 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Mppn, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Handa, M. Kukimoto-Niino, R. Akasaka, S. Kishishita, K. Murayama, T. Terada, M. Inoue, T. Kigawa, S. Kose, N. Imamoto, A. Tanaka, Y. Hayashizaki, M. Shirouzu, S. Yokoyama
The Crystal Structure Of Mouse Nup35 Reveals Atypical Rnp Motifs And Novel Homodimerization Of The Rrm Domain
J. Mol. Biol. V. 363 114 2006
PubMed-ID: 16962612  |  Reference-DOI: 10.1016/J.JMB.2006.07.089
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOPORIN 35
    ChainsA, B, C, D
    EngineeredYES
    FragmentRRM-LIKE DOMAIN
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymNUCLEOPORIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1WWH)

(-) Sites  (0, 0)

(no "Site" information available for 1WWH)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRM_NUP35PS51472 RNA-recognition motif (RRM) Nup35-type domain profile.NUP53_MOUSE169-249  1A:169-249

(-) Exons   (0, 0)

(no "Exon" information available for 1WWH)

(-) Sequences/Alignments

Asymmetric/Biological 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:81
 aligned with NUP53_MOUSE | Q8R4R6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:81
                                   178       188       198       208       218       228       238       248 
          NUP53_MOUSE   169 HLDDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKNVME 249
               SCOP domains d1wwha1 A:169-249 Nucleoporin 35                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeee..hhhhhhhhhhhhhh...eeeeee.....eeeeee.hhhhhhhhhh....ee...ee.eeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM_NUP35  PDB: A:169-249 UniProt: 169-249                                        PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1wwh A 169 HLDDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKNVME 249
                                   178       188       198       208       218       228       238       248 

Chain B from PDB  Type:PROTEIN  Length:79
 aligned with NUP53_MOUSE | Q8R4R6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:79
                                   180       190       200       210       220       230       240         
          NUP53_MOUSE   171 DDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKNVME 249
               SCOP domains d1wwhb_ B: Nucleoporin 35                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhh.....eeee.....eeeee..hhhhhhhhhh....ee...ee.eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM_NUP35  PDB: - UniProt: 169-249                                              PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1wwh B 171 DDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKNVME 249
                                   180       190       200       210       220       230       240         

Chain C from PDB  Type:PROTEIN  Length:79
 aligned with NUP53_MOUSE | Q8R4R6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:79
                                   180       190       200       210       220       230       240         
          NUP53_MOUSE   171 DDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKNVME 249
               SCOP domains d1wwhc_ C: Nucleoporin 35                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhhh.eeeeee.....eeeeee.hhhhhhhhhh....ee...ee.eeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM_NUP35  PDB: - UniProt: 169-249                                              PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 1wwh C 171 DDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKNVME 249
                                   180       190       200       210       220       230       240         

Chain D from PDB  Type:PROTEIN  Length:80
 aligned with NUP53_MOUSE | Q8R4R6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:80
                                   179       189       199       209       219       229       239       249
          NUP53_MOUSE   170 LDDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKNVME 249
               SCOP domains d1wwhd_ D: Nucleoporin 35                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Nup35_RRM-1wwhD01 D:170-249                                                      Pfam domains (1)
           Pfam domains (2) Nup35_RRM-1wwhD02 D:170-249                                                      Pfam domains (2)
           Pfam domains (3) Nup35_RRM-1wwhD03 D:170-249                                                      Pfam domains (3)
           Pfam domains (4) Nup35_RRM-1wwhD04 D:170-249                                                      Pfam domains (4)
         Sec.struct. author hhh.eeeee..hhhhhhhhhhhhhhhh.eeeeee.....eeeeee.hhhhhhhhhh...eee...eeeeeee..hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE RRM_NUP35  PDB: - UniProt: 169-249                                               PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 1wwh D 170 LDDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQARKALSKDGRIFGESIMIGVKPCIDKNVME 249
                                   179       189       199       209       219       229       239       249

   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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WWH)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: RRM (206)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (NUP53_MOUSE | Q8R4R6)
molecular function
    GO:0005487    nucleocytoplasmic transporter activity    Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
biological process
    GO:0006607    NLS-bearing protein import into nucleus    The directed movement of a protein bearing a nuclear localization signal (NLS) from the cytoplasm into the nucleus, across the nuclear membrane.
    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:0006999    nuclear pore organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore.
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
    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:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the 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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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:0044613    nuclear pore central transport channel    The central substructure of the nuclear pore complex (NPC), through which nucleocytoplasmic transport of RNAs, proteins and small molecules occurs. The central transport channel is filled with FG-nucleoporins, which form a selective barrier and provide a series of binding sites for transporter proteins. Characterized S. cerevisiae FG-nucleoporins include Nup159p, Nup145Np, Nup116p, Nup100p, Nsp1p, Nup57p, Nup49p, Nup42p, Nup53p, Nup59p/Asm4p, Nup60p and Nup1. Characterized vertebrate FG-nucleoporins include Nup214, Nup98, Nup62, Nup54, Nup58/45, NLP1, and Nup153.
    GO:0044615    nuclear pore nuclear basket    A filamentous, cage-like assembly on the nuclear face of the nuclear pore complex (NPC). In S. cerevisiae, Mlp1p and Mlp2p are two major components of the NPC nuclear basket. In vertebrates, Tpr is a major component.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
(no "Ligands, Modified Residues, Ions" information available for 1wwh)
 
  Sites
(no "Sites" information available for 1wwh)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wwh)
 

(-) 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
  1wwh
    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
  NUP53_MOUSE | Q8R4R6
    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
  NUP53_MOUSE | Q8R4R6
    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 1WWH)

(-) Related Entries Specified in the PDB File

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