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(-) Description

Title :  CRYSTAL STRUCTURE OF A PAR-6 PDZ-PEPTIDE COMPLEX
 
Authors :  F. C. Peterson, R. R. Penkert, F. B. Volkman, K. E. Prehoda
Date :  29 Dec 03  (Deposition) - 27 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. C. Peterson, R. R. Penkert, B. F. Volkman, K. E. Prehoda
Cdc42 Regulates The Par-6 Pdz Domain Through An Allosteric Crib-Pdz Transition.
Mol. Cell V. 13 665 2004
PubMed-ID: 15023337  |  Reference-DOI: 10.1016/S1097-2765(04)00086-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CG5884-PA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PBH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PAR-6
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: PAR-6
 
Molecule 2 - ACETYLATED VKESLV PEPTIDE
    Chains: B
    Engineered: YES
    Other Details: THIS PROTEIN WAS CHEMICALLY SYNTHESIZED. THE N-TERMINAL HAS BEEN ACETYLATED (ACE)VKESLV.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP

(-) Sites  (0, 0)

(no "Site" information available for 1RZX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RZX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RZX)

(-) Exons   (0, 0)

(no "Exon" information available for 1RZX)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:98
 aligned with O97111_DROME | O97111 from UniProtKB/TrEMBL  Length:351

    Alignment length:98
                                   165       175       185       195       205       215       225       235       245        
         O97111_DROME   156 ETHRRVRLLKHGSDKPLGFYIRDGTSVRVTASGLEKQPGIFISRLVPGGLAESTGLLAVNDEVIEVNGIEVAGKTLDQVTDMMVANSSNLIITVKPAN 253
               SCOP domains d1rzxa_ A: GTPase-binding domain of the cell polarity protein par6 (Par-6B)                        SCOP domains
               CATH domains 1rzxA00 A:156-253  [code=2.30.42.10, no name defined]                                              CATH domains
               Pfam domains ----PDZ-1rzxA01 A:160-250                                                                      --- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeeeee......eeeeeeeeeee...hhhhhhh......eeeee..ee....hhhhhhhhhhhh..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 1rzx A 156 ETHRRVRLLKHGSDKPLGFYIRDGTSVRVTASGLEKQPGIFISRLVPGGLAESTGLLAVNDEVIEVNGIEVAGKTLDQVTDMMVANSSNLIITVKPAN 253
                                   165       175       185       195       205       215       225       235       245        


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....eee Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 1rzx B   1 xVKESLV   7
                            |      
                            1-ACE
   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)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O97111_DROME | O97111)
molecular function
    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:0045176    apical protein localization    Any process in which a protein is transported to, or maintained in, apical regions of the cell.
    GO:0055059    asymmetric neuroblast division    The process resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials.
    GO:0007298    border follicle cell migration    The directed movement of a border cell through the nurse cells to reach the oocyte. An example of this is found in Drosophila melanogaster.
    GO:0060446    branching involved in open tracheal system development    The process in which the anatomical structures of branches in the open tracheal system are generated and organized.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0060429    epithelium development    The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure.
    GO:0045200    establishment of neuroblast polarity    The specification and formation of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system.
    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:0045196    establishment or maintenance of neuroblast polarity    Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system.
    GO:0016332    establishment or maintenance of polarity of embryonic epithelium    Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization of epithelial cells in an embryo.
    GO:0007293    germarium-derived egg chamber formation    Construction of a stage-1 egg chamber in the anterior part of the germarium, from the progeny of germ-line and somatic stem cells. An example of this is found in Drosophila melanogaster.
    GO:0001738    morphogenesis of a polarized epithelium    The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0007309    oocyte axis specification    The establishment, maintenance and elaboration of an axis in the oocyte. An example of this is found in Drosophila melanogaster.
    GO:0006909    phagocytosis    An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
    GO:0051491    positive regulation of filopodium assembly    Any process that activates or increases the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0010592    positive regulation of lamellipodium assembly    Any process that increases the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0007416    synapse assembly    The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional).
    GO:0007430    terminal branching, open tracheal system    Formation of terminal branches in the open tracheal system. These are long cytoplasmic extensions that form fine tubules that transport oxygen directly to the tissues. An example of the process is found in Drosophila melanogaster.
    GO:0045186    zonula adherens assembly    Assembly of the zonula adherens, a cell-cell adherens junction which forms a continuous belt near the apex of epithelial cells.
cellular component
    GO:0045179    apical cortex    The region that lies just beneath the plasma membrane on the apical edge of a cell.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    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:0097482    muscle cell postsynaptic density    A postsynaptic specialization that is part of a neuromuscular junction.
    GO:0035003    subapical complex    The most apical region of the lateral plasma membrane of an invertebrate epithelial cell. The subapical complex lies above the zonula adherens and the septate junction, and is comparable to the position of the tight junction of vertebrate cells.
    GO:0043195    terminal bouton    Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it.

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 Related Entries

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

UniProtKB/TrEMBL
        O97111_DROME | O97111: 1ry4 1x8s 2lc6 2lc7 5i7z

(-) Related Entries Specified in the PDB File

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