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(-) Description

Title :  SOLUTION STRUCTURE OF WW DOMAIN IN WW DOMAIN BINDING PROTEIN 4 (WBP-4)
 
Authors :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Apr 06  (Deposition) - 06 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Ww Domain, Ww Domain-Binding Protein 4, Wbp-4, Formin- Binding Protein 21, 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 :  F. He, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of Ww Domain In Ww Domain Binding Protein 4 (Wbp-4)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - WW DOMAIN-BINDING PROTEIN 4
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050425-06
    Expression System Vector TypePLASMID
    FragmentWW DOMAIN
    GeneWBP4, FBP21
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymWBP-4, FORMIN-BINDING PROTEIN 21

 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 2DK1)

(-) Sites  (0, 0)

(no "Site" information available for 2DK1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DK1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DK1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DK1)

(-) PROSITE Motifs  (2, 4)

NMR Structure (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_2PS50020 WW/rsp5/WWP domain profile.WBP4_HUMAN122-155
163-196
  2A:5-36
A:44-46
2WW_DOMAIN_1PS01159 WW/rsp5/WWP domain signature.WBP4_HUMAN128-153
169-194
  2A:9-34
A:46-46

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003794871ENSE00001481275chr13:41635410-41635811402WBP4_HUMAN1-110--
1.2ENST000003794872ENSE00000817202chr13:41636780-4163685273WBP4_HUMAN1-25250--
1.3ENST000003794873ENSE00000680991chr13:41639152-4163921463WBP4_HUMAN26-46210--
1.4ENST000003794874ENSE00000680992chr13:41639300-41639423124WBP4_HUMAN47-88420--
1.5ENST000003794875ENSE00000680993chr13:41642697-41642873177WBP4_HUMAN88-147601A:1-28 (gaps)43
1.6ENST000003794876ENSE00000680994chr13:41645663-4164570947WBP4_HUMAN147-162161A:28-4316
1.7ENST000003794877ENSE00000680995chr13:41646918-4164699376WBP4_HUMAN163-188261A:44-46 (gaps)25
1.8ENST000003794878ENSE00000817203chr13:41650180-41650373194WBP4_HUMAN188-252651A:47-50 (gaps)11
1.9ENST000003794879ENSE00000680997chr13:41654782-41654945164WBP4_HUMAN253-307550--
1.10ENST0000037948710ENSE00001481264chr13:41656840-416581371298WBP4_HUMAN307-376700--

(-) 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:50
 aligned with WBP4_HUMAN | O75554 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:111
                                   114       124       134       144       154       164       174       184       194       204       214 
           WBP4_HUMAN   105 STSNQQKEKKEKKKRKKDPSKGRWVEGITSEGYHYYYDLISGASQWEKPEGFQGDLKKTAVKTVWVEGLSEDGFTYYYNTETGESRWEKPDDFIPHTSDLPSSKVNENSLG 215
               SCOP domains ---------------------d2dk1a1 A:7-44                        ---------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....---------------....eee.........eee.....ee..............----------------------..-----------------...-------. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------WW_DOMAIN_2  PDB: A:5-36          -------WW_DOMAIN_2  PDB: A:44-46         ------------------- PROSITE (1)
                PROSITE (2) -----------------------WW_DOMAIN_1  PDB: A:9-34  ---------------WW_DOMAIN_1  PDB: A:46-46 --------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.5  PDB: A:1-28 (gaps) [INCOMPLETE]  ---------------Exon 1.7 UniProt: 163-188 --------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.6        -------------------------Exon 1.8  PDB: A:47-50 (gaps Transcript 1 (2)
                 2dk1 A   1 GSSG---------------SSGRWVEGITSEGYHYYYDLISGASQWEKPEGFQGDLKKT----------------------SG-----------------PSS-------G  50
                               |     -         5        15        25        35        |-         -         - ||      -         -| |      -|
                               4               5                                     44                     45|                47 |      50
                                                                                                             46                  49        

   Legend:   → Mismatch (orange background)
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    → 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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DK1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DK1)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (WBP4_HUMAN | O75554)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0070064    proline-rich region binding    Interacting selectively and non-covalently with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein.
    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).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0045292    mRNA cis splicing, via spliceosome    The joining together, after removal of an intervening sequence composed of one or more introns, of two segments of the same RNA molecule via spliceosomal catalysis to produce an mRNA composed only of exon sequences that all came from the same primary transcript.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
cellular component
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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.
    GO:0005681    spliceosomal complex    Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.

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 Related Entries

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

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        WBP4_HUMAN | O755542jxw

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