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(-) Description

Title :  CRYSTAL STRUCTURE OF BROMODOMAIN 2 OF MOUSE BRD4
 
Authors :  F. Vollmuth, W. Blankenfeldt, M. Geyer
Date :  17 Sep 09  (Deposition) - 13 Oct 09  (Release) - 05 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Bromodomain, Alpha Helical, N-Acetyl Lysine Binding Domain, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Vollmuth, W. Blankenfeldt, M. Geyer
Structures Of The Dual Bromodomains Of The P-Tefb-Activating Protein Brd4 At Atomic Resolution
J. Biol. Chem. V. 284 36547 2009
PubMed-ID: 19828451  |  Reference-DOI: 10.1074/JBC.M109.033712
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 4
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPPROEX-HTB
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentBROMODOMAIN 2, UNP RESIDUES 349-464
    GeneBRD4
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMITOTIC CHROMOSOME-ASSOCIATED PROTEIN, MCAP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:65 , HOH A:108 , CYS A:357 , ARG A:454BINDING SITE FOR RESIDUE BME A 1
2AC2SOFTWARECYS A:392 , ILE A:395 , LYS A:396 , PRO A:398 , EDO A:467BINDING SITE FOR RESIDUE BME A 465
3AC3SOFTWAREHOH A:143 , ILE A:394 , ILE A:395 , LYS A:396 , HIS A:397 , ASN A:429 , LYS A:432 , ASP A:460BINDING SITE FOR RESIDUE EDO A 466
4AC4SOFTWAREHOH A:112 , PRO A:380 , VAL A:381 , BME A:465BINDING SITE FOR RESIDUE EDO A 467

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.BRD4_MOUSE75-147
369-441
  1-
A:369-441

(-) Exons   (0, 0)

(no "Exon" information available for 3JVM)

(-) 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 BRD4_MOUSE | Q9ESU6 from UniProtKB/Swiss-Prot  Length:1400

    Alignment length:144
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456    
           BRD4_MOUSE   317 AKLGPRRESSRPVKPPKKDVPDSQQHPGPEKSSKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD 460
               SCOP domains d3jv                            ma_ A: automated matches                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------------------Bromodomain-3jvmA01 A:358-446                                                            -------------- Pfam domains
         Sec.struct. author ....----------------------------...hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------BROMODOMAIN_2  PDB: A:369-441 UniProt: 369-441                           ------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3jvm A 345 GAMG----------------------------SKISEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLESREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD 460
                               |     -         -         -  |    356       366       376       386       396       406       416       426       436       446       456    
                             348                          349                                                                                                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3JVM)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BRD4_MOUSE | Q9ESU6)
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:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0044154    histone H3-K14 acetylation    The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 14 of the histone.
    GO:0043983    histone H4-K12 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 12 of the histone.
    GO:0001833    inner cell mass cell proliferation    The proliferation of cells in the inner cell mass.
    GO:0043388    positive regulation of DNA binding    Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0010971    positive regulation of G2/M transition of mitotic cell cycle    Any process that increases the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:1901407    regulation of phosphorylation of RNA polymerase II C-terminal domain    Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain.
    GO:0000083    regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
    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:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0008024    cyclin/CDK positive transcription elongation factor complex    A transcription elongation factor complex that facilitates the transition from abortive to productive elongation by phosphorylating the CTD domain of the large subunit of DNA-directed RNA polymerase II, holoenzyme. Contains a cyclin and a cyclin-dependent protein kinase catalytic subunit.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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
        BRD4_MOUSE | Q9ESU62dww 2jns 3jvj 3jvk 3jvl 3muk 3mul

(-) Related Entries Specified in the PDB File

3jvj 3jvk 3jvl