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

(-) Description

Title :  CRYSTAL STRUCTURE OF THE BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF
 
Authors :  P. Filippakopoulos, S. Picaud, T. Keates, E. Ugochukwu, F. Von Delf, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, S. Knapp, Stru Genomics Consortium (Sgc)
Date :  29 Nov 11  (Deposition) - 18 Jan 12  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A
Keywords :  Bromodomain, Bptf, Falz, Fac1, Bromodomain And Phd Finger-Containing Transcription Factor, Fetal Alz-50 Clone 1 Protein, Fetal Alzheimer Antigen, Structural Genomics Consortium, Sgc, Transcription (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 - BROMODOMAIN OF HUMAN NUCLEOSOME-REMODELING FACTOR SUBUNIT BPTF
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 2914-3037
    GeneBPTF, FAC1, FALZ
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBROMODOMAIN AND PHD FINGER-CONTAINING TRANSCRIPTION FACTOR

 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
17PE1Ligand/Ion2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:14 , HOH A:188 , PRO A:2825 , ASP A:2834 , TYR A:2880 , ASN A:2881 , PHE A:2887BINDING SITE FOR RESIDUE 7PE A 0

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UV2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3UV2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UV2)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.BPTF_HUMAN2944-3014  1A:2818-2888
2BROMODOMAIN_1PS00633 Bromodomain signature.BPTF_HUMAN2949-3006  1A:2823-2880

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003218921cENSE00001357454chr17:65821780-65822453674BPTF_HUMAN1-2052050--
1.2ENST000003218922ENSE00001148014chr17:65850056-65850878823BPTF_HUMAN205-4792750--
1.3ENST000003218923ENSE00001148007chr17:65862580-65862803224BPTF_HUMAN479-554760--
1.4ENST000003218924ENSE00001147999chr17:65870933-65871136204BPTF_HUMAN554-622690--
1.5ENST000003218925ENSE00001147993chr17:65871672-65871860189BPTF_HUMAN622-685640--
1.7ENST000003218927ENSE00001147984chr17:65882244-65882432189BPTF_HUMAN685-748640--
1.8ENST000003218928ENSE00001147980chr17:65887960-65888150191BPTF_HUMAN748-811640--
1.9ENST000003218929ENSE00001223583chr17:65889486-65889841356BPTF_HUMAN812-9301190--
1.10ENST0000032189210ENSE00001612408chr17:65890150-65890281132BPTF_HUMAN930-974450--
1.11ENST0000032189211ENSE00002166039chr17:65899905-65900034130BPTF_HUMAN974-1017440--
1.12ENST0000032189212ENSE00001750925chr17:65900818-65900956139BPTF_HUMAN1018-1064470--
1.13ENST0000032189213ENSE00001665602chr17:65905698-65905877180BPTF_HUMAN1064-1124610--
1.14ENST0000032189214ENSE00001606591chr17:65906993-659093032311BPTF_HUMAN1124-18947710--
1.15ENST0000032189215ENSE00001657056chr17:65914830-65914954125BPTF_HUMAN1894-1936430--
1.16ENST0000032189216ENSE00001625445chr17:65916131-65916259129BPTF_HUMAN1936-1979440--
1.17ENST0000032189217ENSE00001642854chr17:65918956-65919106151BPTF_HUMAN1979-2029510--
1.18ENST0000032189218ENSE00001783568chr17:65920663-6592070543BPTF_HUMAN2029-2043150--
1.19ENST0000032189219ENSE00001604847chr17:65924471-65924717247BPTF_HUMAN2044-2126830--
1.20ENST0000032189220ENSE00001680408chr17:65925452-65925603152BPTF_HUMAN2126-2176510--
1.21ENST0000032189221ENSE00001779718chr17:65928027-65928135109BPTF_HUMAN2177-2213370--
1.22ENST0000032189222ENSE00001770472chr17:65936555-65936772218BPTF_HUMAN2213-2285730--
1.23aENST0000032189223aENSE00001733774chr17:65940266-65940488223BPTF_HUMAN2286-2360750--
1.24cENST0000032189224cENSE00001223457chr17:65941525-65942441917BPTF_HUMAN2360-26653060--
1.25ENST0000032189225ENSE00001603899chr17:65943842-6594392483BPTF_HUMAN2666-2693280--
1.26ENST0000032189226ENSE00001707553chr17:65944197-65944422226BPTF_HUMAN2693-2768760--
1.27aENST0000032189227aENSE00001743235chr17:65955657-65955991335BPTF_HUMAN2769-28801120--
1.29ENST0000032189229ENSE00001707648chr17:65960328-65960520193BPTF_HUMAN2880-2944651A:2793-281826
1.30ENST0000032189230ENSE00001598996chr17:65962688-6596277285BPTF_HUMAN2945-2973291A:2819-284729
1.31ENST0000032189231ENSE00001755666chr17:65971888-65972074187BPTF_HUMAN2973-3035631A:2847-290963
1.32cENST0000032189232cENSE00001766345chr17:65978368-659804942127BPTF_HUMAN3035-3046121A:2909-29113

(-) 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:119
 aligned with BPTF_HUMAN | Q12830 from UniProtKB/Swiss-Prot  Length:3046

    Alignment length:119
                                  2928      2938      2948      2958      2968      2978      2988      2998      3008      3018      3028         
          BPTF_HUMAN   2919 EDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFKASRSH 3037
               SCOP domains d3uv2a_ A: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------BROMODOMAIN_2  PDB: A:2818-2888 UniProt: 2944-3014                     ----------------------- PROSITE (1)
                PROSITE (2) ------------------------------BROMODOMAIN_1  PDB: A:2823-2880 UniProt: 2949-3006        ------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.29  PDB: A:2793-281Exon 1.30  PDB: A:2819-2847  -------------------------------------------------------------1.3 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.31  PDB: A:2847-2909 UniProt: 2973-3035                 -- Transcript 1 (2)
                3uv2 A 2793 EDAMTVLTPLTEKDYEGLKRVLRSLQAHKMAWPFLEPVDPNDAPDYYGVIKEPMDLATMEERVQRRYYEKLTEFVADMTKIFDNCRYYNPSDSPFYQCAEVLESFFVQKLKGFKASRSH 2911
                                  2802      2812      2822      2832      2842      2852      2862      2872      2882      2892      2902         

   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 3UV2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UV2)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BPTF_HUMAN | Q12830)
molecular function
    GO:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:1990090    cellular response to nerve growth factor stimulus    A process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nerve growth factor stimulus.
    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:0001892    embryonic placenta development    The embryonically driven 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:0007492    endoderm development    The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces 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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009611    response to wounding    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 indicating damage to the organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0016589    NURF complex    An ISWI complex that contains an ATPase subunit of the ISWI family (SNF2L in mammals), a NURF301 homolog (BPTF in humans), and additional subunits, though the composition of these additional subunits varies slightly with species. NURF is involved in regulation of transcription from TRNA polymerase II promoters.
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

 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
    7PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3uv2)
 

(-) 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
  3uv2
    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
  BPTF_HUMAN | Q12830
    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
  BPTF_HUMAN | Q12830
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BPTF_HUMAN | Q128302f6j 2f6n 2fsa 2fui 2fuu 2ri7 3qzs 3qzt 3qzv

(-) Related Entries Specified in the PDB File

3uv4 3uv5 3uvd 3uvw 3uvx 3uvy 3uw9