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(-) Description

Title :  SOLUTION STRUCTURE OF THE PDZ DOMAIN OF PDZ AND LIM DOMAIN 2
 
Authors :  R. Hatta, F. Hayashi, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Feb 04  (Deposition) - 30 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pdz Domain Pdz-Lim Protein, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Hatta, F. Hayashi, M. Yoshida, S. Yokoyama
Solution Structure Of The Pdz Domain Of Pdz And Lim Domain 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PDZ AND LIM DOMAIN 2
    Chains: A
    Engineered: YES
    Expression System Plasmid: P030203-89
    Expression System Vector Type: PLASMID
    Fragment: PDZ DOMAIN
    Gene: CDNA 2310041E13
    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 1VB7)

(-) Sites  (0, 0)

(no "Site" information available for 1VB7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VB7)

(-) Cis Peptide Bonds  (3, 60)

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:14 -Pro A:15
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ala A:16 -Pro A:17
31, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Ser A:79 -Pro A:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VB7)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PDLI2_MOUSE1-84  1A:8-88

(-) Exons   (0, 0)

(no "Exon" information available for 1VB7)

(-) 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:94
 aligned with PDLI2_MOUSE | Q8R1G6 from UniProtKB/Swiss-Prot  Length:349

    Alignment length:94
                                 1                                                                                        
                                 |   5        15        25        35        45        55        65        75        85    
           PDLI2_MOUSE    - -----MALTVDVAGPAPWGFRISGGRDFHTPIIVTKVTERGKAEAADLRPGDIIVAINGQSAENMLHAEAQSKIRQSASPLRLQLDRSQTASPG 89
               SCOP domains d1vb7a_ A: PDZ-LIM protein mystique                                                            SCOP domains
               CATH domains 1vb7A00 A:1-94  [code=2.30.42.10, no name defined]                                             CATH domains
               Pfam domains -------PDZ-1vb7A01 A:8-86                                                             -------- Pfam domains
         Sec.struct. author .......eeeee..........eee....eeee........hhhhhh.....eeeee..ee....hhhhhhhhhhh....eeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----PDZ  PDB: A:8-88 UniProt: 1-84                                                      ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  1vb7 A  1 GSSGSSGLTVDVAGPAPWGFRISGGRDFHTPIIVTKVTERGKAEAADLRPGDIIVAINGQSAENMLHAEAQSKIRQSASPLRLQLDRSSGPSSG 94
                                    10        20        30        40        50        60        70        80        90
   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  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (PDLI2_MOUSE | Q8R1G6)
molecular function
    GO:0051393    alpha-actinin binding    Interacting selectively and non-covalently with alpha-actinin, one of a family of proteins that cross-link F-actin as antiparallel homodimers. Alpha-actinin has a molecular mass of 93-103 KDa; at the N-terminus there are two calponin homology domains, at the C-terminus there are two EF-hands. These two domains are connected by the rod domain. This domain is formed by triple-helical spectrin repeats.
    GO:0031005    filamin binding    Interacting selectively and non-covalently with a filamin, any member of a family of high molecular mass cytoskeletal proteins that crosslink actin filaments to form networks and stress fibers. Filamins contain an amino-terminal alpha-actinin-like actin binding domain, which is followed by a rod-domain composed of 4 to 24 100-residue repetitive segments including a carboxy-terminal dimerization domain.
    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:0032036    myosin heavy chain binding    Interacting selectively and non-covalently with a heavy chain of a myosin complex.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0030864    cortical actin cytoskeleton    The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0001725    stress fiber    A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.

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  Cis Peptide Bonds
    Ala A:16 - Pro A:17   [ RasMol ]  
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    Ser A:79 - Pro A:80   [ RasMol ]  
 

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