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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SIXTH BROMODOMAIN OF HUMAN POLY-BROMODOMAIN CONTAINING PROTEIN 1 (PB1)
 
Authors :  P. Filippakopoulos, T. Keates, S. Picaud, A. C. W. Pike, E. Ugochukwu, F Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, S. Knap Structural Genomics Consortium (Sgc)
Date :  30 Aug 09  (Deposition) - 22 Sep 09  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A
Keywords :  Pb1, Polybromo 1 Isoform 1, Baf180, Polybromo0Id, Pbrm1, Brg1- Associated Factor 180, Structural Genomics, Sgc, Structural Genomics Consortium, Bromodomain, Chromatin Regulator, Dna-Binding, Nucleus, Phosphoprotein, Transcription, Transcription Regulation (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 - PROTEIN POLYBROMO-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)-R3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PB1, PBRM1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPB1, POLYBROMO-1D, BRG1-ASSOCIATED FACTOR 180, BAF180

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
3ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:50 , PHE A:813 , GLU A:817 , TYR A:861BINDING SITE FOR RESIDUE EDO A 900
2AC2SOFTWAREARG A:801 , GLN A:838 , VAL A:870 , GLU A:871 , ARG A:874BINDING SITE FOR RESIDUE EDO A 901
3AC3SOFTWAREHOH A:132 , ILE A:775 , PRO A:776 , ASN A:823BINDING SITE FOR RESIDUE EDO A 902
4AC4SOFTWAREHIS A:751 , GLU A:798BINDING SITE FOR RESIDUE ZN A 950

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IU6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IU6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_064675Y893CPB1_HUMANPolymorphism753344888AY861C
2UniProtVAR_064676T895SPB1_HUMANUnclassified  ---AT863S
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.PB1_HUMAN64-134
200-270
400-470
538-608
676-746
817-862		  1-
-
-
-
-
A:785-830

(-) Exons   (0, 0)

(no "Exon" information available for 3IU6)

(-) 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:143
 aligned with PB1_HUMAN | Q86U86 from UniProtKB/Swiss-Prot  Length:1689

    Alignment length:143
                                   781       791       801       811       821       831       841       851       861       871       881       891       901       911   
            PB1_HUMAN   772 PNVTLLIQELIHNLFVSVMSHQDDEGRCYSDSLAEIPAVDPNFPNKPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDELCKNGEILLSPALSYTTKHLHNDVEKERKEKLPKEI 914
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.......hhhhhhh...............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------C-S------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------BROMODOMAIN_2  PDB: A:785-830 UniProt: 817-862---------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3iu6 A 740 MNVTLLIQELIHNLFVSVMSHQDDEGRcYSDSLAEIPAVDPNFPNKPPLTFDIIRKNVENNRYRRLDLFQEHMFEVLERARRMNRTDSEIYEDAVELQQFFIKIRDELCKNGEILLSPALSYTTKHLHNDVEKERKEKLPKEI 882
                                   749       759       769       779       789       799       809       819       829       839       849       859       869       879   
                                                     767-OCS
   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 3IU6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IU6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IU6)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PB1_HUMAN | Q86U86)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0090544    BAF-type complex    A SWI/SNF-type complex that contains a subunit from the BAF (Brahma-Associated Factor) family.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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  3iu6
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  PB1_HUMAN | Q86U86
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 Related Entries

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

UniProtKB/Swiss-Prot
        PB1_HUMAN | Q86U86: 2ktb 3g0j 3hmf 3iu5 3k2j 3ljw 3mb4 3tlp 4q0n 4q0o 4y03 5e7d 5fh6 5fh7 5fh8 5hrv 5hrw 5hrx 5ii1 5ii2 5iid

(-) Related Entries Specified in the PDB File

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