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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BHC80 PHD FINGER
 
Authors :  J. R. Horton, X. Cheng, R. E. Collins
Date :  09 May 07  (Deposition) - 14 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.43
Chains :  Asym./Biol. Unit :  A,B,E
Keywords :  Phd Finger, Histone Code, Braf-Hdac Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Lan, R. E. Collins, R. De Cegli, R. Alpatov, J. R. Horton, X. Shi, O. Gozani, X. Cheng, Y. Shi
Recognition Of Unmethylated Histone H3 Lysine 4 Links Bhc80 To Lsd1-Mediated Gene Repression.
Nature V. 448 718 2007
PubMed-ID: 17687328  |  Reference-DOI: 10.1038/NATURE06034
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHD FINGER PROTEIN 21A
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET28B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GenePHF21A, BHC80, KIAA1696
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBRAF35-HDAC COMPLEX PROTEIN BHC80, BHC80A
 
Molecule 2 - HISTONE H3
    ChainsE
    EngineeredYES
    FragmentH3 1-10
    Other DetailsSYNTHESIZED PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:491 , CYS A:494 , HIS A:511 , CYS A:514BINDING SITE FOR RESIDUE ZN A 355
2AC2SOFTWARECYS A:503 , CYS A:506 , CYS A:529 , CYS A:532BINDING SITE FOR RESIDUE ZN A 356
3AC3SOFTWARECYS B:491 , CYS B:494 , HIS B:511 , CYS B:514BINDING SITE FOR RESIDUE ZN B 357
4AC4SOFTWARECYS B:503 , CYS B:506 , CYS B:529 , CYS B:532BINDING SITE FOR RESIDUE ZN B 358

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:516 -Pro A:517
2Asp B:516 -Pro B:517

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.PF21A_HUMAN488-535
 
  2A:488-535
B:488-535
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.PF21A_HUMAN491-532
 
  2A:491-532
B:491-532

(-) Exons   (0, 0)

(no "Exon" information available for 2PUY)

(-) 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:59
 aligned with PF21A_HUMAN | Q96BD5 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:59
                                   494       504       514       524       534         
          PF21A_HUMAN   485 DIHEDFCSVCRKSGQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKKEEAI 543
               SCOP domains d2puya_ A: automated matches                                SCOP domains
               CATH domains 2puyA00 A:485-543                                           CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ................ee......eehhhhh.............hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ZF_PHD_2  PDB: A:488-535 UniProt: 488-535       -------- PROSITE (1)
                PROSITE (2) ------ZF_PHD_1  PDB: A:491-532 UniProt: 491-532 ----------- PROSITE (2)
                 Transcript ----------------------------------------------------------- Transcript
                 2puy A 485 MIHEDFCSVCRKSGQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKKEEAI 543
                                   494       504       514       524       534         

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with PF21A_HUMAN | Q96BD5 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:60
                                   493       503       513       523       533       543
          PF21A_HUMAN   484 GDIHEDFCSVCRKSGQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKKEEAI 543
               SCOP domains d2puyb_ B: automated matches                                 SCOP domains
               CATH domains 2puyB00 B:484-543                                            CATH domains
           Pfam domains (1) ------PHD-2puyB01 B:490-535                         -------- Pfam domains (1)
           Pfam domains (2) ------PHD-2puyB02 B:490-535                         -------- Pfam domains (2)
         Sec.struct. author ..............eeeee......eehhhhh.............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----ZF_PHD_2  PDB: B:488-535 UniProt: 488-535       -------- PROSITE (1)
                PROSITE (2) -------ZF_PHD_1  PDB: B:491-532 UniProt: 491-532 ----------- PROSITE (2)
                 Transcript ------------------------------------------------------------ Transcript
                 2puy B 484 HMIHEDFCSVCRKSGQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQMLKKEEAI 543
                                   493       503       513       523       533       543

Chain E from PDB  Type:PROTEIN  Length:10
 aligned with H3_ZYGBA | P61836 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:10
                                    11
             H3_ZYGBA     2 ARTKQTARKS  11
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author ..eeee.... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 2puy E   1 ARTKQTARKS  10
                                    10

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Family: PHD (44)
1aPHD-2puyB01B:490-535
1bPHD-2puyB02B:490-535

(-) Gene Ontology  (21, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PF21A_HUMAN | Q96BD5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    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:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    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:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    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: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:1990391    DNA repair complex    A protein complex involved in DNA repair processes including direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    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.

Chain E   (H3_ZYGBA | P61836)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
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:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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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        H3_ZYGBA | P618362fuu
        PF21A_HUMAN | Q96BD52yql

(-) Related Entries Specified in the PDB File

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