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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SECOND BROMODOMAIN OF PLECKSTRIN HOMOLOGY DOMAIN INTERACTING PROTEIN (PHIP)
 
Authors :  P. Filippakopoulos, S. Picaud, T. Keates, E. Ugochukwu, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, S. Knapp, Stru Genomics Consortium (Sgc)
Date :  25 Mar 10  (Deposition) - 14 Apr 10  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Phip, Pleckstrin Homology Domain Interacting Protein, Dcaf14, Ndrp, Ddb1 And Cul4 Associated Factor 14, Sgc, Structural Genomics Consortium, Bromodomain, Phosphoprotein, Wd Repeat, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Filippakopoulos, S. Picaud, M. Mangos, T. Keates, J. P. Lambert, D. Barsyte-Lovejoy, I. Felletar, R. Volkmer, S. Muller, T. Pawson, A. C. Gingras, C. H. Arrowsmith, S. Knapp
Histone Recognition And Large-Scale Structural Analysis Of The Human Bromodomain Family.
Cell(Cambridge, Mass. ) V. 149 214 2012
PubMed-ID: 22464331  |  Reference-DOI: 10.1016/J.CELL.2012.02.013

(-) Compounds

Molecule 1 - PH-INTERACTING PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1302-1434
    GenePHIP, WDR11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHIP, IRS-1 PH DOMAIN-BINDING PROTEIN, WD REPEAT-CONTAINING PROTEIN 11

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MB31Ligand/Ion1-METHYLPYRROLIDIN-2-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:41 , HOH A:90 , HOH A:151 , HOH A:152 , PRO A:1340 , VAL A:1345 , TYR A:1350BINDING SITE FOR RESIDUE MB3 A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MB3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MB3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MB3)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.PHIP_HUMAN1176-1246
1333-1403
  1-
A:1333-1403
2BROMODOMAIN_1PS00633 Bromodomain signature.PHIP_HUMAN1338-1395  1A:1338-1395

(-) Exons   (0, 0)

(no "Exon" information available for 3MB3)

(-) 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:116
 aligned with PHIP_HUMAN | Q8WWQ0 from UniProtKB/Swiss-Prot  Length:1821

    Alignment length:116
                                  1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      
          PHIP_HUMAN   1316 YDIQAWKKQCEELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSDYKSALRF 1431
               SCOP domains d3mb3a_ A: automated matches                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------Bromodomain-3mb3A01 A:1325-1409                                                      ---------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------BROMODOMAIN_2  PDB: A:1333-1403 UniProt: 1333-1403                     ---------------------------- PROSITE (1)
                PROSITE (2) ----------------------BROMODOMAIN_1  PDB: A:1338-1395 UniProt: 1338-1395        ------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                3mb3 A 1316 YDIQAWKKQCEELLNLIFQCEDSEPFRQPVDLLEYPDYRDIIDTPMDFATVRETLEAGNYESPMELCKDVRLIFSNSKAYTPSKRSRIYSMSLRLSAFFEEHISSVLSDYKSALRF 1431
                                  1325      1335      1345      1355      1365      1375      1385      1395      1405      1415      1425      

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MB3)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHIP_HUMAN | Q8WWQ0)
molecular function
    GO:0005158    insulin receptor binding    Interacting selectively and non-covalently with the insulin receptor.
    GO:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    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:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:2001237    negative regulation of extrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0043568    positive regulation of insulin-like growth factor receptor signaling pathway    Any process that increases the frequency, rate or extent of insulin-like growth factor receptor signaling.
    GO:0045840    positive regulation of mitotic nuclear division    Any process that activates or increases the frequency, rate or extent of mitosis.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0022604    regulation of cell morphogenesis    Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0001932    regulation of protein phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
cellular component
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHIP_HUMAN | Q8WWQ05enb 5enc 5ene 5enf 5enh 5eni 5enj

(-) Related Entries Specified in the PDB File

3mb4