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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST WW DOMAIN OF FBP11 / HYPA (FBP11 WW1) COMPLEXED WITH A PL (PPLP) MOTIF PEPTIDE LIGAND
 
Authors :  Y. Kato, T. Miyakawa, J. Kurita, M. Tanokura
Date :  11 Sep 06  (Deposition) - 24 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Ww Domain, Complex, Fbp11, Hypa, Pl Motif, Pplp Motif, Nmr, Solution Structure, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kato, T. Miyakawa, J. Kurita, M. Tanokura
Complex Structure Of Fbp11 Ww1 And A Pl Ligand Reveals The Mechanism Of Proline-Rich Ligand Recognition By Group-Ii/Iii Ww Domains
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HUNTINGTIN-INTERACTING PROTEIN HYPA/FBP11
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: THE FIRST WW DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PRE-MRNA-PROCESSING FACTOR 40 HOMOLOG A, FORMIN- BINDING PROTEIN 3, HUNTINGTIN YEAST PARTNER A, FAS LIGAND- ASSOCIATED FACTOR 1, NY-REN-6 ANTIGEN
 
Molecule 2 - PL (PPLP) MOTIF PEPTIDE FROM MYOSIN TAIL REGION- INTERACTING PROTEIN MTI1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PROTEIN BBC1

 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 2DYF)

(-) Sites  (0, 0)

(no "Site" information available for 2DYF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WW_DOMAIN_1PS01159 WW/rsp5/WWP domain signature.PR40A_HUMAN146-171
187-212		  1A:12-37
-

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YJL020C1YJL020C.1X:402404-3989313474BBC1_YEAST1-115711571B:1-9 (gaps)24

(-) 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:30
 aligned with PR40A_HUMAN | O75400 from UniProtKB/Swiss-Prot  Length:957

    Alignment length:33
                                   150       160       170   
          PR40A_HUMAN   141 GAKSMWTEHKSPDGRTYYYNTETKQSTWEKPDD 173
               SCOP domains d2   dyfa_ A: automated matches   SCOP domains
               CATH domains --------------------------------- CATH domains
               Pfam domains --------------------------------- Pfam domains
         Sec.struct. author ..---eeeee.....eeeee....eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------- SAPs(SNPs)
                    PROSITE -----WW_DOMAIN_1  PDB: A:12-37 -- PROSITE
                 Transcript --------------------------------- Transcript
                 2dyf A  10 GS---WTEHKSPDGRTYYYNTETKQSTWEKPDD  39
                             |   |  16        26        36   
                            11  12                           


Chain B from PDB  Type:PROTEIN  Length:9
 aligned with BBC1_YEAST | P47068 from UniProtKB/Swiss-Prot  Length:1157

    Alignment length:24
                                   788       798    
           BBC1_YEAST   779 SSAPLPPVSEEYHPMPNTAPPLPR 802
               SCOP domains ------------------------ SCOP domains
               CATH domains ------------------------ CATH domains
               Pfam domains ------------------------ Pfam domains
         Sec.struct. author ..---------------....... Sec.struct. author
                 SAPs(SNPs) ------------------------ SAPs(SNPs)
                    PROSITE ------------------------ PROSITE
               Transcript 1 Exon 1.1 UniProt: 1-1157 Transcript 1
                 2dyf B   1 GS---------------TAPPLPR   9
                             |       -       | 5    
                             2               3
   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 2DYF)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 27)

NMR Structure(hide GO term definitions)
Chain A   (PR40A_HUMAN | O75400)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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).
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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    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.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0032465    regulation of cytokinesis    Any process that modulates the frequency, rate or extent of the division of the cytoplasm of a cell and its separation into two daughter cells.
cellular component
    GO:0005685    U1 snRNP    A ribonucleoprotein complex that contains small nuclear RNA U1.
    GO:0071004    U2-type prespliceosome    A spliceosomal complex that is formed by association of the 5' splice site with the U1 snRNP, while the branch point sequence is recognized by the U2 snRNP. The prespliceosome includes many proteins in addition to those found in the U1 and U2 snRNPs. Commitment to a given pair of 5' and 3' splice sites occurs at the time of prespliceosome formation.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.

Chain B   (BBC1_YEAST | P47068)
molecular function
    GO:0017024    myosin I binding    Interacting selectively and non-covalently with a class I myosin; myosin I heavy chains are single-headed, possess tails of various lengths, and do not self-associate into bipolar filaments.
    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:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
cellular component
    GO:0030479    actin cortical patch    An endocytic patch that consists of an actin-containing structure found at the plasma membrane in cells; formed of networks of branched actin filaments that lie just beneath the plasma membrane and assemble, move, and disassemble rapidly. An example of this is the actin cortical patch found in Saccharomyces cerevisiae.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BBC1_YEAST | P47068: 1tg0 1wdx 1zuk
        PR40A_HUMAN | O75400: 1uzc 1ywi 1ywj 1zr7 2cqn 2kzg 2l5f 2l9v 2lks

(-) Related Entries Specified in the PDB File

1zr7 LIGAND-FREE FORM OF FBP11 WW1