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(-) Description

Title :  MOLECULAR BASIS OF HISTONE H3K36ME3 RECOGNITION BY THE PWWP DOMAIN OF BRPF1.
 
Authors :  A. Vezzoli, N. Bonadies, M. D. Allen, S. M. V. Freund, C. M. Santiveri, B. Kvinlaug, B. J. P. Huntly, B. Gottgens, M. Bycroft
Date :  02 Feb 10  (Deposition) - 21 Apr 10  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Metal-Binding, Zinc-Finger, Chromatin Regulator, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Vezzoli, N. Bonadies, M. D. Allen, S. M. V. Freund, C. M. Santiveri, B. Kvinlaug, B. J. P. Huntly, B. Gottgens, M. Bycroft
Molecular Basis Of Histone H3K36Me3 Recognition By The Pwwp Domain Of Brpf1.
Nat. Struct. Mol. Biol. V. 17 617 2010
PubMed-ID: 20400950  |  Reference-DOI: 10.1038/NSMB.1797

(-) Compounds

Molecule 1 - PEREGRIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainC41
    Expression System Taxid562
    Expression System VectorPRSETA
    FragmentRESIDUES 1076-1205
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBRPF1 PWWP DOMAIN, BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1, PROTEIN BR140
 
Molecule 2 - HISTONE H3.2
    ChainsB
    FragmentRESIDUES 23-43
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTRIMETHYLATION AT POSITION 36
    SynonymHUMAN H3 HISTONE, H3/M, H3/O
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2M3L1Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1093 , ARG A:1094 , LEU A:1157 , LYS A:1161 , HOH A:2121 , PRO B:38BINDING SITE FOR RESIDUE FMT A2205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X4W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X4W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_028232G1117EBRPF1_HUMANPolymorphism1042294AG1117E
2UniProtVAR_048430H1193QBRPF1_HUMANPolymorphism36081837AH1193Q

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PWWPPS50812 PWWP domain profile.BRPF1_HUMAN1085-1168  1A:1085-1168

(-) Exons   (0, 0)

(no "Exon" information available for 2X4W)

(-) 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:125
 aligned with BRPF1_HUMAN | P55201 from UniProtKB/Swiss-Prot  Length:1214

    Alignment length:125
                                  1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199     
         BRPF1_HUMAN   1080 DSPLDALDLVWAKCRGYPSYPALIIDPKMPREGMFHHGVPIPVPPLEVLKLGEQMTQEAREHLYLVLFFDNKRTWQWLPRTKLVPLGVNQDLDKEKMLEGRKSNIRKSVQIAYHRALQHRSKVQG 1204
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---PWWP-2x4wA01 A:1083-1182                                                                            ---------------------- Pfam domains
         Sec.struct. author ........eeee.......eeeeee........eee..eee...hhhhhhhhhhhhhhhh...eeeee......eeeehhh.eee...hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------E---------------------------------------------------------------------------Q----------- SAPs(SNPs)
                    PROSITE -----PWWP  PDB: A:1085-1168 UniProt: 1085-1168                                           ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                2x4w A 1080 DSPLDALDLVWAKCRGYPSYPALIIDPKMPREGMFHHGVPIPVPPLEVLKLGEQMTQEAREHLYLVLFFDNKRTWQWLPRTKLVPLGVNQDLDKEKMLEGRKSNIRKSVQIAYHRALQHRSKVQG 1204
                                  1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199     

Chain B from PDB  Type:PROTEIN  Length:13
 aligned with H32_HUMAN | Q71DI3 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:13
                                    38   
           H32_HUMAN     29 SAPATGGVKKPHR   41
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                2x4w B   28 SAPATGGVkKPHR   40
                                    37   
                                   36-M3L

   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 2X4W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X4W)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Tudor (88)
(-)
Family: PWWP (17)

(-) Gene Ontology  (26, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BRPF1_HUMAN | P55201)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    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:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    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:0070776    MOZ/MORF histone acetyltransferase complex    A histone acetyltransferase complex that has histone H3 acetyltransferase and coactivator activities. Subunits of the human complex include MYST3/MOZ, MYST4/MORF, ING5, EAF6 and one of BRPF1, BRD1/BRPF2 and BRPF3.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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 B   (H32_HUMAN | Q71DI3)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
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:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
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: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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        BRPF1_HUMAN | P552012d9e 2rs9 2x35 2x4x 2x4y 3l42 3mo8 4lc2 4qyd 4qyl 4uye 5c6s 5c7n 5c85 5c87 5c89 5d7x 5dy7 5dya 5dyc 5e3d 5e3g 5em3 5epr 5eps 5eq1 5erc 5etb 5etd 5ev9 5eva 5ewc 5ewd 5ewh 5ewv 5eww 5ffv 5ffw 5ffy 5fg4 5fg5 5g4r 5g4s 5t4u 5t4v
        H32_HUMAN | Q71DI32iij 2x4x 2x4y 3av1 3db3 3mo8 3qo2 3r93 4mzf 4mzg 4mzh 4ouc 5b0y 5b0z 5b40 5bo0 5ciu 5vac

(-) Related Entries Specified in the PDB File

2d9e SOLUTION STRUCTURE OF THE BROMODOMAIN OF PEREGRIN
2x35 MOLECULAR BASIS OF HISTONE H3K36ME3 RECOGNITION BY THE PWWP DOMAIN OF BRPF1.
2x4x MOLECULAR BASIS OF HISTONE H3K36ME3 RECOGNITION BY THE PWWP DOMAIN OF BRPF1.
2x4y MOLECULAR BASIS OF HISTONE H3K36ME3 RECOGNITION BY THE PWWP DOMAIN OF BRPF1.