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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIFTH BROMODOMAIN FROM MOUSE POLYBROMO-1
 
Authors :  R. Sano, F. Hayashi, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Bromodomain, Four Helices, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sano, F. Hayashi, M. Yoshida, S. Yokoyama
Solution Structure Of The Fifth Bromodomain From Mouse Polybromo-1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYBROMO-1
    Chains: A
    Engineered: YES
    Expression System Plasmid: P060821-09
    Expression System Vector Type: PLASMID
    Fragment: BROMODOMAIN
    Gene: PB1
    Mutation: YES
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: CELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2YQD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YQD)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.PB1_MOUSE64-134
200-270
400-470
538-608
676-746
817-862		  1-
-
-
-
A:34-104
-
2BROMODOMAIN_1PS00633 Bromodomain signature.PB1_MOUSE72-126
205-262
405-462
548-600
681-738		  1-
-
-
-
A:39-96

(-) Exons   (0, 0)

(no "Exon" information available for 2YQD)

(-) Sequences/Alignments

NMR Structure
   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:120
 aligned with PB1_MOUSE | Q8BSQ9 from UniProtKB/Swiss-Prot  Length:1634

    Alignment length:159
                                   613       623       633       643       653       663       673       683       693       703       713       723       733       743       753         
            PB1_MOUSE   604 GSQVYNDAHILEKLLKDKRKELGPLPDDDDMASPKLKLSRKSGVSPKKSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRD 762
               SCOP domains d2                                       yqda_ A: automated matches                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------Bromodomain-2yqdA01 A:24-108                                                         ------------ Pfam domains
         Sec.struct. author ..---------------------------------------.............hhhhhhhhhhhhhhh........hhhhh.......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BROMO-------------------------------------------------------------------BROMODOMAIN_2  PDB: A:34-104 UniProt: 676-746                          ---------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------BROMODOMAIN_1  PDB: A:39-96 UniProt: 681-738              ------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yqd A   1 GS---------------------------------------SGSSGKKSKYMTPMQQKLNEVYEAVKNYTDKRGRRLSAIFLRLPSRSELPDYYLTIKKPMDMEKIRSHMMANKYQDIDSMVEDFVMMFNNACTYNEPESLIYKDALVLHKVLLETRRD 120
                             |       -         -         -         - |      11        21        31        41        51        61        71        81        91       101       111         
                             2                                       3
   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)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: Bromodomain] (56)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (PB1_MOUSE | Q8BSQ9)
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:0001974    blood vessel remodeling    The reorganization or renovation of existing blood vessels.
    GO:0060948    cardiac vascular smooth muscle cell development    The process whose specific outcome is the progression of a cardiac vascular smooth muscle cell over time, from its formation to the mature state.
    GO:0003349    epicardium-derived cardiac endothelial cell differentiation    The process in which an epicardial cell acquires the specialized structural and/or functional features of a cardiac endothelial cell.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0003007    heart morphogenesis    The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    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: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.
    GO:0060979    vasculogenesis involved in coronary vascular morphogenesis    The differentiation of endothelial cells from progenitor cells that contributes to blood vessel development in the heart, and the de novo formation of blood vessels and tubes.
cellular component
    GO:0090544    BAF-type complex    A SWI/SNF-type complex that contains a subunit from the BAF (Brahma-Associated Factor) family.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    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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