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(-) Description

Title :  SOLUTION STRUCTURE OF PDZ DOMAIN OF MOUSE CYPHER PROTEIN
 
Authors :  M. Sato, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 May 04  (Deposition) - 29 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain, Signal Transduction, A Striated Muscle-Specific Pdzlim Domain, Lim Domain Binding 3, Zasp, Z-Band Alternatively Spliced Pdz-Motif Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sato, N. Tochio, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of Pdz Domain Of Mouse Cypher Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYPHER PROTEIN
    Chains: A
    Engineered: YES
    Expression System Plasmid: P031104-22
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN
    Gene: RIKEN CDNA 1110032B18
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    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 1WJL)

(-) Sites  (0, 0)

(no "Site" information available for 1WJL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gly A:16 -Pro A:17
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gly A:18 -Pro A:19

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.LDB3_MOUSE1-84  1A:8-90

(-) Exons   (0, 0)

(no "Exon" information available for 1WJL)

(-) 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:90
 aligned with LDB3_MOUSE | Q9JKS4 from UniProtKB/Swiss-Prot  Length:723

    Alignment length:90
                                   1                                                                                  
                                   | 3        13        23        33        43        53        63        73        83
            LDB3_MOUSE    - -------MSYSVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQKS 83
               SCOP domains d1wjla_ A: Zasp (Cypher, Oracle 1)                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------PDZ-1wjlA01 A:10-88                                                            -- Pfam domains
         Sec.struct. author ........eeeeeee......eee...........eeee...hhhhhh......eeeee........hhhhhhhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------PDZ  PDB: A:8-90 UniProt: 1-84                                                      PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                  1wjl A  1 GSSGSSGMSYSVTLTGPGPWGFRLQGGKDFNMPLTISRITPGSKAAQSQLSQGDLVVAIDGVNTDTMTHLEAQNKIKSASYNLSLTLQKS 90
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
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  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 1WJL)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (LDB3_MOUSE | Q9JKS4)
molecular function
    GO:0008092    cytoskeletal protein binding    Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0051371    muscle alpha-actinin binding    Interacting selectively and non-covalently with muscle isoforms of actinin. Muscle alpha-actinin isoforms are found in skeletal and cardiac muscle and are localized to the Z-disc.
    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:0005080    protein kinase C binding    Interacting selectively and non-covalently with protein kinase C.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0045214    sarcomere organization    The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs.
cellular component
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0031143    pseudopodium    A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.

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    Gly A:16 - Pro A:17   [ RasMol ]  
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