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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 5TH PDZ DOMAIN OF INAD
 
Authors :  R. Ranganathan, M. Socolich
Date :  11 Jul 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (2x),B (2x)
Keywords :  Pdz Domain, Scaffolding Protein, Disulfide-Bond, Membrane, Sensory Transduction, Vision, Signaling Protein, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Mishra, M. Socolich, M. A. Wall, J. Graves, Z. Wang, R. Ranganathan
Dynamic Scaffolding In A G Protein-Coupled Signaling System.
Cell(Cambridge, Mass. ) V. 131 80 2007
PubMed-ID: 17923089  |  Reference-DOI: 10.1016/J.CELL.2007.07.037
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INACTIVATION-NO-AFTER-POTENTIAL D PROTEIN
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-5X-3
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Fragment5TH PDZ DOMAIN
    GeneINAD
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2QKT)

(-) Sites  (0, 0)

(no "Site" information available for 2QKT)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:606 -A:645
2B:606 -B:645

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.INAD_DROME17-106
249-332
364-448
584-664
 
489-552
  2-
-
-
A:584-664
B:584-664
-
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.INAD_DROME17-106
249-332
364-448
584-664
 
489-552
  4-
-
-
A:584-664
B:584-664
-

(-) Exons   (0, 0)

(no "Exon" information available for 2QKT)

(-) Sequences/Alignments

Asymmetric 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:85
 aligned with INAD_DROME | Q24008 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:85
                                   589       599       609       619       629       639       649       659     
           INAD_DROME   580 LEKFNVDLMKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSMEVTRPK 664
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........eeeeee..eeeeeee....hhhhhhhh....eeeee..ee....hhhhhhh.......eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: A:584-664 UniProt: 584-664                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2qkt A 580 LEKFNVDLMKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSMEVTRPK 664
                                   589       599       609       619       629       639       649       659     

Chain B from PDB  Type:PROTEIN  Length:85
 aligned with INAD_DROME | Q24008 from UniProtKB/Swiss-Prot  Length:674

    Alignment length:85
                                   589       599       609       619       629       639       649       659     
           INAD_DROME   580 LEKFNVDLMKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSMEVTRPK 664
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----PDZ-2qktB01 B:584-661                                                         --- Pfam domains (1)
           Pfam domains (2) ----PDZ-2qktB02 B:584-661                                                         --- Pfam domains (2)
         Sec.struct. author ..eeeeeeee.......eeeeee..eeeeeee....hhhhhh......eeeee..ee.....hhhhhhh.....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----PDZ  PDB: B:584-664 UniProt: 584-664                                              PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2qkt B 580 LEKFNVDLMKKAGKELGLSLSPNEIGCTIADLIQGQYPEIDSKLQRGDIITKFNGDALEGLPFQVCYALFKGANGKVSMEVTRPK 664
                                   589       599       609       619       629       639       649       659     

   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  (0, 0)

(no "SCOP Domain" information available for 2QKT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (INAD_DROME | Q24008)
molecular function
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0031473    myosin III binding    Interacting selectively and non-covalently with a class III myosin; myosin III is monomeric and has an N terminal kinase domain.
    GO:0017022    myosin binding    Interacting selectively and non-covalently with any part of a myosin complex; myosins are any of a superfamily of molecular motor proteins that bind to actin and use the energy of ATP hydrolysis to generate force and movement along actin filaments.
    GO:0009881    photoreceptor activity    The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
    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:0030159    receptor signaling complex scaffold activity    Functions to provide a physical support for the assembly of a multiprotein receptor signaling complex.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
    GO:0071482    cellular response to light stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
    GO:0016059    deactivation of rhodopsin mediated signaling    The process of restoring the photoreceptor cell to its unexcited state after termination of the stimulus (photon).
    GO:0050962    detection of light stimulus involved in sensory perception    The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light.
    GO:0007602    phototransduction    The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
    GO:0008104    protein localization    Any process in which a protein is transported to, or maintained in, a specific location.
    GO:0050896    response to stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0016027    inaD signaling complex    A complex of proteins that are involved in phototransduction and attached to the transient receptor potential (TRP) channel. The protein connections are mediated through inaD.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0016028    rhabdomere    The specialized microvilli-containing organelle on the apical surfaces of a photoreceptor cell containing the visual pigment rhodopsin and most of the proteins involved in phototransduction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        INAD_DROME | Q240081ihj 2la8 2qku 2qkv 3r0h 5f67

(-) Related Entries Specified in the PDB File

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