Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF RCB DOMAIN OF IRSP53
 
Authors :  K. Murayama, S. Suetsugu, A. Seto, M. Shirouzu, T. Takenawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  21 May 04  (Deposition) - 07 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cellular Signaling Protein, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Murayama, S. Suetsugu, A. Seto, M. Shirouzu, T. Takenawa, S. Yokoyama
Crystal Structure Of Rcb Domain Of Irsp53
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INSULIN RECEPTOR SUBSTRATE P53
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-4T-1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIRSP53

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1WDZ)

(-) Sites  (0, 0)

(no "Site" information available for 1WDZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003213001cENSE00001380542chr17:79008962-79009108147BAIP2_HUMAN1-18182A:2-18
B:2-18
17
17
1.2ENST000003213002ENSE00001262168chr17:79027468-7902754376BAIP2_HUMAN19-44262A:19-44
B:19-44
26
26
1.3ENST000003213003ENSE00001262156chr17:79031681-7903176787BAIP2_HUMAN44-73302A:44-73
B:44-73
30
30
1.4ENST000003213004ENSE00001262308chr17:79058632-7905869362BAIP2_HUMAN73-93212A:73-93
B:73-93
21
21
1.5bENST000003213005bENSE00001262060chr17:79059454-7905952572BAIP2_HUMAN94-117242A:94-117
B:94-117
24
24
1.6ENST000003213006ENSE00001262138chr17:79060243-79060380138BAIP2_HUMAN118-163462A:118-163
B:118-163 (gaps)
46
46
1.8ENST000003213008ENSE00001262131chr17:79073728-79073880153BAIP2_HUMAN164-214512A:164-214
B:164-214
51
51
1.9ENST000003213009ENSE00001262122chr17:79077302-79077523222BAIP2_HUMAN215-288742A:215-232
B:215-232
18
18
1.10ENST0000032130010ENSE00001262113chr17:79077707-79077908202BAIP2_HUMAN289-356680--
1.11ENST0000032130011ENSE00001262052chr17:79078314-79078515202BAIP2_HUMAN356-423680--
1.12ENST0000032130012ENSE00001262105chr17:79079878-7907994669BAIP2_HUMAN423-446240--
1.13ENST0000032130013ENSE00001262100chr17:79080545-79080707163BAIP2_HUMAN446-500550--
1.14ENST0000032130014ENSE00001262093chr17:79082275-7908230935BAIP2_HUMAN501-512120--
1.17aENST0000032130017aENSE00001262042chr17:79089570-7908961748BAIP2_HUMAN512-528170--
1.17dENST0000032130017dENSE00001262211chr17:79090030-790912321203BAIP2_HUMAN528-552250--

(-) 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:231
 aligned with BAIP2_HUMAN | Q9UQB8 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 
          BAIP2_HUMAN     2 SLSRSEEMHRLTENVYKTIMEQFNPSLRNFIAMGKNYEKALAGVTYAAKGYFDALVKMGELASESQGSKELGDVLFQMAEVHRQIQNQLEEMLKSFHNELLTQLEQKVELDSRYLSAALKKYQTEQRSKGDALDKCQAELKKLRKKSQGSKNPQKYSDKELQYIDAISNKQGELENYVSDGYKTALTEERRRFCFLVEKQCAVAKNSAAYHSKGKELLAQKLPLWQQACAD 232
               SCOP domains d1wdza1 A:2-228 BAP2/IRSp53 N-terminal domain                                                                                                                                                                                      ---- SCOP domains
               CATH domains 1wdzA00 A:2-232 Bai1-associated protein 2 isoform 1                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c        Exon 1.2  PDB: A:19-44    ----------------------------Exon 1.4  PDB: A:73-9Exon 1.5b  PDB: A:94-117Exon 1.6  PDB: A:118-163 UniProt: 118-163     Exon 1.8  PDB: A:164-214 UniProt: 164-214          Exon 1.9           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.3  PDB: A:44-73        --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1wdz A   2 SLSRSEEMHRLTENVYKTIMEQFNPSLRNFIAMGKNYEKALAGVTYAAKGYFDALVKMGELASESQGSKELGDVLFQMAEVHRQIQNQLEEMLKSFHNELLTQLEQKVELDSRYLSAALKKYQTEQRSKGDALDKCQAELKKLRKKSQGSKNPQKYSDKELQYIDAISNKQGELENYVSDGYKTALTEERRRFCFLVEKQCAVAKNSAAYHSKGKELLAQKLPLWQQGVDS 232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 

Chain B from PDB  Type:PROTEIN  Length:222
 aligned with BAIP2_HUMAN | Q9UQB8 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231 
          BAIP2_HUMAN     2 SLSRSEEMHRLTENVYKTIMEQFNPSLRNFIAMGKNYEKALAGVTYAAKGYFDALVKMGELASESQGSKELGDVLFQMAEVHRQIQNQLEEMLKSFHNELLTQLEQKVELDSRYLSAALKKYQTEQRSKGDALDKCQAELKKLRKKSQGSKNPQKYSDKELQYIDAISNKQGELENYVSDGYKTALTEERRRFCFLVEKQCAVAKNSAAYHSKGKELLAQKLPLWQQACAD 232
               SCOP domains d1wdzb_ B: BAP2/IRSp53 N-terminal domain                                                                                                                                                                                                SCOP domains
               CATH domains 1wdzB00 B:2-232 Bai1-associated protein 2 isoform 1                                                                                                                                                                                     CATH domains
           Pfam domains (1) ---------------IMD-1wdzB01 B:17-228                                                                                                                                                                                                ---- Pfam domains (1)
           Pfam domains (2) ---------------IMD-1wdzB02 B:17-228                                                                                                                                                                                                ---- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...---------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c        Exon 1.2  PDB: B:19-44    ----------------------------Exon 1.4  PDB: B:73-9Exon 1.5b  PDB: B:94-117Exon 1.6  PDB: B:118-163 (gaps)               Exon 1.8  PDB: B:164-214 UniProt: 164-214          Exon 1.9           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.3  PDB: B:44-73        --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1wdz B   2 SLSRSEEMHRLTENVYKTIMEQFNPSLRNFIAMGKNYEKALAGVTYAAKGYFDALVKMGELASESQGSKELGDVLFQMAEVHRQIQNQLEEMLKSFHNELLTQLEQKVELDSRYLSAALKKYQTEQRSKGDALDKCQAELKKLRKKSQ---------DKELQYIDAISNKQGELENYVSDGYKTALTEERRRFCFLVEKQCAVAKNSAAYHSKGKELLAQKLPLWQQGVDS 232
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       | -       161       171       181       191       201       211       221       231 
                                                                                                                                                                             149       159                                                                         

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Family: IMD (2)
1aIMD-1wdzB01B:17-228
1bIMD-1wdzB02B:17-228

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BAIP2_HUMAN | Q9UQB8)
molecular function
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0008093    cytoskeletal adaptor activity    The binding activity of a molecule that brings together a cytoskeletal protein and one or more other molecules, permitting them to function in a coordinated way.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0070064    proline-rich region binding    Interacting selectively and non-covalently with a proline-rich region, i.e. a region that contains a high proportion of proline residues, in a protein.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0051764    actin crosslink formation    The process in which two or more actin filaments are connected together by proteins that act as crosslinks between the filaments. The crosslinked filaments may be on the same or differing axes.
    GO:0051017    actin filament bundle assembly    The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0007009    plasma membrane organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.
    GO:2000251    positive regulation of actin cytoskeleton reorganization    Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
    GO:0030838    positive regulation of actin filament polymerization    Any process that activates or increases the frequency, rate or extent of actin polymerization.
    GO:0061003    positive regulation of dendritic spine morphogenesis    Any process that increases the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0048167    regulation of synaptic plasticity    A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    GO:0009617    response to bacterium    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 from a bacterium.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
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: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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    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:0030175    filopodium    Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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:0014069    postsynaptic density of dendrite    An electron dense network of proteins within and adjacent to the postsynaptic membrane of the dendrite of asymetric synapses. Its major components include neurotransmitter receptors and the proteins that spatially and functionally organize them such as anchoring and scaffolding molecules, signaling enzymes and cytoskeletal components.
    GO:0001726    ruffle    Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  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 1wdz)
 
  Sites
(no "Sites" information available for 1wdz)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wdz)
 

(-) 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
  1wdz
    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
  BAIP2_HUMAN | Q9UQB8
    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
  BAIP2_HUMAN | Q9UQB8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BAIP2_HUMAN | Q9UQB81y2o 2ykt 3rnj 4js0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WDZ)