Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF PAR-3 PDZ3
 
Authors :  W. Feng, H. Wu, L. Chan, M. Zhang
Date :  18 Mar 08  (Deposition) - 10 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Par-3, Pdz Domain, Scaffold Protein, Cell Polarity, Alternative Splicing, Cell Cycle, Cell Division, Cell Junction, Coiled Coil, Membrane, Phosphoprotein, Tight Junction, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Feng, H. Wu, L. Chan, M. Zhang
Solution Structure Of Par-3 Pdz3
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PARTITIONING-DEFECTIVE 3 HOMOLOG
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System VectorPET32A
    Expression System Vector TypePLASMID
    FragmentPDZ 3 DOMAIN
    GenePARD3, PAR3
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    SynonymPARD-3, PAR-3, ATYPICAL PKC ISOTYPE-SPECIFIC- INTERACTING PROTEIN, ASIP, ATYPICAL PKC-SPECIFIC-BINDING PROTEIN, ASBP

 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 2K1Z)

(-) Sites  (0, 0)

(no "Site" information available for 2K1Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K1Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K1Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K1Z)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.PARD3_RAT271-347
461-546
590-665
  1-
-
A:15-90

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENSRNOT000000426233ENSRNOE00000226378chr19:57248705-57248885181PARD3_RAT1-61610--
1.4ENSRNOT000000426234ENSRNOE00000226366chr19:57274660-57274838179PARD3_RAT61-120600--
1.5ENSRNOT000000426235ENSRNOE00000226359chr19:57291996-57292127132PARD3_RAT121-164440--
1.6ENSRNOT000000426236ENSRNOE00000226349chr19:57323542-5732363392PARD3_RAT165-195310--
1.7ENSRNOT000000426237ENSRNOE00000226023chr19:57326051-5732613484PARD3_RAT195-223290--
1.8ENSRNOT000000426238ENSRNOE00000226017chr19:57336953-57337078126PARD3_RAT223-265430--
1.9ENSRNOT000000426239ENSRNOE00000226004chr19:57338261-57338643383PARD3_RAT265-3931290--
1.10ENSRNOT0000004262310ENSRNOE00000226001chr19:57343038-57343177140PARD3_RAT393-439470--
1.11ENSRNOT0000004262311ENSRNOE00000225992chr19:57345075-57345203129PARD3_RAT440-482430--
1.12ENSRNOT0000004262312ENSRNOE00000225986chr19:57347421-5734745939PARD3_RAT483-495130--
1.13ENSRNOT0000004262313ENSRNOE00000289127chr19:57356718-57356906189PARD3_RAT496-558630--
1.21ENSRNOT0000004262321ENSRNOE00000348454chr19:57372710-5737277263PARD3_RAT559-579210--
1.22ENSRNOT0000004262322ENSRNOE00000315922chr19:57372991-5737301323PARD3_RAT580-58781A:7-126
1.23ENSRNOT0000004262323ENSRNOE00000298920chr19:57373120-5737319273PARD3_RAT587-611251A:12-3625
1.25aENSRNOT0000004262325aENSRNOE00000364088chr19:57375674-57375824151PARD3_RAT612-662511A:37-8751
1.26ENSRNOT0000004262326ENSRNOE00000194939chr19:57382265-57382454190PARD3_RAT662-725641A:87-11024
1.27ENSRNOT0000004262327ENSRNOE00000194947chr19:57389269-57389420152PARD3_RAT725-776520--
1.28ENSRNOT0000004262328ENSRNOE00000194956chr19:57390436-5739048045PARD3_RAT776-791160--
1.29ENSRNOT0000004262329ENSRNOE00000194966chr19:57394613-57394840228PARD3_RAT791-867770--
1.30ENSRNOT0000004262330ENSRNOE00000194972chr19:57407487-57407718232PARD3_RAT867-944780--
1.32ENSRNOT0000004262332ENSRNOE00000225936chr19:57441539-57441649111PARD3_RAT944-981380--
1.33ENSRNOT0000004262333ENSRNOE00000225927chr19:57455445-57455681237PARD3_RAT981-1060800--
1.34ENSRNOT0000004262334ENSRNOE00000225922chr19:57586456-57586576121PARD3_RAT1060-1100410--
1.35ENSRNOT0000004262335ENSRNOE00000225918chr19:57596635-57596762128PARD3_RAT1101-1143430--
1.36bENSRNOT0000004262336bENSRNOE00000455094chr19:57601563-576031331571PARD3_RAT1143-12561140--

(-) 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:104
 aligned with PARD3_RAT | Q9Z340 from UniProtKB/Swiss-Prot  Length:1337

    Alignment length:104
                                   591       601       611       621       631       641       651       661       671       681    
            PARD3_RAT   582 GTREFLTFEVPLNDSGSAGLGVSVKGNRSKENHADLGIFVKSIINGGAASKDGRLRVNDQLIAVNGESLLGKANQEAMETLRRSMSTEGNKRGMIQLIVARRIS 685
               SCOP domains d2k1za_ A: automated matches                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------PDZ-2k1zA01 A:15-105                                                                       ----- Pfam domains
         Sec.struct. author .eeeeeeeee...........eeeeeee......eeeeeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhhhhhh......eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PDZ  PDB: A:15-90 UniProt: 590-665                                          -------------------- PROSITE
           Transcript 1 (1) 1.22  ------------------------Exon 1.25a  PDB: A:37-87 UniProt: 612-662          ----------------------- Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.23  PDB: A:12-36  --------------------------------------------------Exon 1.26  PDB: A:87-110 Transcript 1 (2)
                 2k1z A   7 GTREFLTFEVPLNDSGSAGLGVSVKGNRSKENHADLGIFVKSIINGGAASKDGRLRVNDQLIAVNGESLLGKANQEAMETLRRSMSTEGNKRGMIQLIVARRIS 110
                                    16        26        36        46        56        66        76        86        96       106    

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2K1Z)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (30, 30)

NMR Structure(hide GO term definitions)
Chain A   (PARD3_RAT | Q9Z340)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005547    phosphatidylinositol-3,4,5-trisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,4,5-trisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3', 4' and 5' positions.
    GO:0032266    phosphatidylinositol-3-phosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
    GO:0005546    phosphatidylinositol-4,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-4,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 4' and 5' positions.
    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:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
biological process
    GO:0070830    bicellular tight junction assembly    The aggregation, arrangement and bonding together of a set of components to form a tight junction, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet.
    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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    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:0090162    establishment of epithelial cell polarity    The specification and formation of anisotropic intracellular organization of an epithelial cell.
    GO:0045197    establishment or maintenance of epithelial cell apical/basal polarity    Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of an epithelial cell.
    GO:0022011    myelination in peripheral nervous system    The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of Schwann cells in the peripheral nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0010801    negative regulation of peptidyl-threonine phosphorylation    Any process that decreases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0031643    positive regulation of myelination    Any process that activates or increases the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0060341    regulation of cellular localization    Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell.
cellular component
    GO:0044295    axonal growth cone    The migrating motile tip of a growing nerve cell axon.
    GO:0005923    bicellular tight junction    An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
    GO:0005938    cell cortex    The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
    GO:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    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:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0033269    internode region of axon    An axon part that is located between the nodes of Ranvier and surrounded by compact myelin sheath.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

 Visualization

(-) Interactive Views

NMR Structure
  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 2k1z)
 
  Sites
(no "Sites" information available for 2k1z)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2k1z)
 

(-) 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
  2k1z
    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
  PARD3_RAT | Q9Z340
    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
  PARD3_RAT | Q9Z340
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PARD3_RAT | Q9Z3402k20 2ns5 2ogp 3zee 4dc2 4i6p

(-) Related Entries Specified in the PDB File

2k20 SAME PROTEIN IN COMPLEX WITH PTEN PEPTIDE