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(-) Description

Title :  SOLUTION STRUCTURE OF THE TUDOR DOMAIN OF PHD FINGER PROTEIN 1 (PHF1 PROTEIN)
 
Authors :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  22 Dec 06  (Deposition) - 26 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Tudor Domain, Phd Finger Protein 1, Phf1 Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Dang, Y. Muto, M. Inoue, T. Kigawa, M. Shirouzu, T. Terada, S. Yokoyama
Solution Structure Of The Tudor Domain Of Phd Finger Protein 1 (Phf1 Protein)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHD FINGER PROTEIN 1
    ChainsA
    EngineeredYES
    Expression System PlasmidP050822-22
    Expression System Vector TypePLASMID
    FragmentTUDOR DOMAIN, RESIDUES 8-62
    GenePHF1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS
    SynonymPROTEIN PHF1

 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 2E5P)

(-) Sites  (0, 0)

(no "Site" information available for 2E5P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E5P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E5P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_044500T42SPHF1_HUMANPolymorphism6934613AT21S

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

(-) PROSITE Motifs  (2, 1)

NMR Structure (2, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.PHF1_HUMAN87-142  1A:65-68
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.PHF1_HUMAN90-139
189-237
  1A:65-68
-

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2dENST000003745162dENSE00001882125chr6:33378738-33378992255PHF1_HUMAN-00--
1.3ENST000003745163ENSE00002164760chr6:33380025-33380199175PHF1_HUMAN1-53531A:1-32 (gaps)43
1.4aENST000003745164aENSE00002187959chr6:33380285-3338036682PHF1_HUMAN54-81281A:33-6028
1.5bENST000003745165bENSE00002140212chr6:33380475-3338057096PHF1_HUMAN81-113331A:60-645
1.6cENST000003745166cENSE00002181210chr6:33380973-33381073101PHF1_HUMAN113-146341A:65-684
1.7aENST000003745167aENSE00002159642chr6:33381186-33381334149PHF1_HUMAN147-196500--
1.7cENST000003745167cENSE00002147742chr6:33381513-3338160896PHF1_HUMAN196-228330--
1.8ENST000003745168ENSE00002156748chr6:33381818-3338188669PHF1_HUMAN228-251240--
1.9aENST000003745169aENSE00002187072chr6:33382020-33382143124PHF1_HUMAN251-292420--
1.10ENST0000037451610ENSE00002170495chr6:33382254-3338232168PHF1_HUMAN293-315230--
1.11aENST0000037451611aENSE00002200067chr6:33382502-33382606105PHF1_HUMAN315-350360--
1.11dENST0000037451611dENSE00002183383chr6:33382732-33382921190PHF1_HUMAN350-413640--
1.12aENST0000037451612aENSE00002164572chr6:33383012-3338310695PHF1_HUMAN414-445320--
1.12eENST0000037451612eENSE00002172770chr6:33383367-3338344781PHF1_HUMAN445-472280--
1.13gENST0000037451613gENSE00002142059chr6:33383587-33384230644PHF1_HUMAN472-567960--

(-) 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:68
 aligned with PHF1_HUMAN | O43189 from UniProtKB/Swiss-Prot  Length:567

    Alignment length:117
                                    20        30        40        50        60        70        80        90       100       110       120       
           PHF1_HUMAN    11 GASSLWDPASPAPTSGPRPRLWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAALPGEELLCCVCRSETVVPGNRLVSCEKCRHAYHQDCHVPRAPAPG 127
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...---------......--.....eeeee.....eeeeeeeeee....eeeeee...eeeeee...ee......--------------------------------------.... Sec.struct. author
                 SAPs(SNPs) -------------------------------S------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------ZF_PHD_2  PDB: A:65-68 UniProt: 87-142    PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------ZF_PHD_1  PDB: A:65-68 UniProt: 90-139 PROSITE (2)
           Transcript 1 (1) Exon 1.3  PDB: A:1-32 (gaps) UniProt: 1-53 Exon 1.4a  PDB: A:33-60     -------------------------------Exon 1.6c       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.5b  PDB: A:60-64          -------------- Transcript 1 (2)
                 2e5p A   1 GSS---------GSSGPR--LWEGQDVLARWTDGLLYLGTIKKVDSAREVCLVQFEDDSQFLVLWKDISPAALSG--------------------------------------PSSG  68
                              |      -  |    | -|       19        29        39        49        59    |    -         -         -         -   |   
                              3         4    9 10                                                    64                                     65   

   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  (0, 0)

(no "SCOP Domain" information available for 2E5P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E5P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E5P)

(-) Gene Ontology  (19, 19)

NMR Structure(hide GO term definitions)
Chain A   (PHF1_HUMAN | O43189)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0061086    negative regulation of histone H3-K27 methylation    Any process that decreases the rate, frequency, or extent of histone H3-K27 methylation. Histone H3-K27 methylation is the modification of histone H3 by addition of a methyl group to lysine at position 27 of the histone.
    GO:0061087    positive regulation of histone H3-K27 methylation    Any process that increases the rate, frequency, or extent of histone H3-K27 methylation. Histone H3-K27 methylation is the modification of histone H3 by addition of a methyl group to lysine at position 27 of the histone.
    GO:0031060    regulation of histone methylation    Any process that modulates the frequency, rate or extent of the covalent addition of methyl groups to histones.
    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:0035098    ESC/E(Z) complex    A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    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:0035861    site of double-strand break    A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.

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 Related Entries

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        PHF1_HUMAN | O431892m0o 4hcz

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