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 CATALYTIC CORE DOMAIN OF HUMAN PHF8
 
Authors :  L. Yu, Y. Wang, S. Huang, J. Wang, Z. Deng, W. Wu, W. Gong, Z. Chen
Date :  03 Oct 09  (Deposition) - 19 Jan 10  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Phf8 (Phd Finger Protein 8), Histone Demethylase, Chromatin Modification, Methylated H3K9, Mental Retardation, Metal-Binding, Phosphoprotein, Zinc-Finger, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Yu, Y. Wang, S. Huang, J. Wang, Z. Deng, Q. Zhang, W. Wu, X. Zhang, Z. Liu, W. Gong, Z. Chen
Structural Insights Into A Novel Histone Demethylase Phf8
Cell Res. V. 20 166 2010
PubMed-ID: 20101266  |  Reference-DOI: 10.1038/CR.2010.8

(-) Compounds

Molecule 1 - PHD FINGER PROTEIN 8
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainROSETTA 2 (DE3) CELLS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES IN UNP 86-447
    GenePHF8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPHF8

 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
1FE21Ligand/IonFE (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:8 , HOH A:19 , HOH A:43 , HIS A:247 , ASP A:249 , HIS A:319BINDING SITE FOR RESIDUE FE2 A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K3N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K3N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_062250F315SPHF8_HUMANDisease (MRXSSD)121918524AF279S

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1JMJCPS51184 JmjC domain profile.PHF8_HUMAN231-387  1A:195-351

(-) Exons   (0, 0)

(no "Exon" information available for 3K3N)

(-) 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:349
 aligned with PHF8_HUMAN | Q9UPP1 from UniProtKB/Swiss-Prot  Length:1060

    Alignment length:354
                                   137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477    
           PHF8_HUMAN   128 RSRTFDSSDEVILKPTGNQLTVEFLEENSFSVPILVLKKDGLGMTLPSPSFTVRDVEHYVGSDKEIDVIDVTRQADCKMKLGDFVKYYYSGKREKVLNVISLEFSDTRLSNLVETPKIVRKLSWVENLWPEECVFERPNVQKYCLMSVRDSYTDFHIDFGGTSVWYHVLKGEKIFYLIRPTNANLTLFECWSSSSNQNEMFFGDQVDKCYKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIEKRLSTADLFRFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHEDEIPETVRTVQLIKDLAREIRLVEDIFQ 481
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------JmjC-3k3nA01 A:234-334                                                                               --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhh.........hhhhhhhhh....eee...............hhhhhhhhhh.-.eeeeee....eeeeeehhhhhhhhh.......eeeeeee....hhhhh...hhhhhhhhhhhhhh.............eeeee...eeeeee.hhhhheeeeeeeeeeeeeeee..hhhhhhhhhhhhh..hhhhhhhhhh....eeeeee...eeee....eeeeeeeeeeeeeeeee....hhhhhhhhhhhhhhhh----....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------JMJC  PDB: A:195-351 UniProt: 231-387                                                                                                                        ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k3n A  92 RSRTFDSSDEVILKPTGNQLTVEFLEENSFSVPILVLKKDGLGMTLPSPSFTVRDVEHYVGS-KEIDVIDVTRQADCKMKLGDFVKYYYSGKREKVLNVISLEFSDTRLSNLVETPKIVRKLSWVENLWPEECVFERPNVQKYCLMSVRDSYTDFHIDFGGTSVWYHVLKGEKIFYLIRPTNANLTLFECWSSSSNQNEMFFGDQVDKCYKCSVKQGQTLFIPTGWIHAVLTPVDCLAFGGNFLHSLNIEMQLKAYEIEKRLS----FRFPNFETICWYVGKHILDIFRGLRENRRHPASYLVHGGKALNLAFRAWTRKEALPDHEDEIPETVRTVQLIKDLAREIRLVEDIFQ 445
                                   101       111       121       131       141       151 | |   161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351  |    361       371       381       391       401       411       421       431       441    
                                                                                       153 |                                                                                                                                                                                                    354  359                                                                                      
                                                                                         155                                                                                                                                                                                                                                                                                                  

   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 3K3N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K3N)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (31, 31)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PHF8_HUMAN | Q9UPP1)
molecular function
    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:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0032452    histone demethylase activity    Catalysis of the removal of a methyl group from a histone.
    GO:0071558    histone demethylase activity (H3-K27 specific)    Catalysis of the removal of a methyl group from lysine at position 27 of the histone H3 protein.
    GO:0051864    histone demethylase activity (H3-K36 specific)    Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 36) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 36 of the histone H3 protein.
    GO:0032454    histone demethylase activity (H3-K9 specific)    Catalysis of the reaction: histone H3 N6-methyl-L-lysine (position 9) + alpha-ketoglutarate + O2 = succinate + CO2 + formaldehyde + lysine. This reaction is the removal of a methyl group from lysine at position 9 of the histone H3 protein.
    GO:0035575    histone demethylase activity (H4-K20 specific)    Catalysis of the reaction: histone H4 N6-methyl-L-lysine (position 20) + 2-oxoglutarate + O2 = histone H4 L-lysine (position 20) + succinate + formaldehyde + CO2. This reaction is the removal of a methyl group from lysine at position 20 of the histone H4 protein.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016706    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors    Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
    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:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0071557    histone H3-K27 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone.
    GO:0070544    histone H3-K36 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 36 of the histone.
    GO:0033169    histone H3-K9 demethylation    The modification of histone H3 by the removal of a methyl group from lysine at position 9 of the histone.
    GO:0035574    histone H4-K20 demethylation    The modification of histone H4 by the removal of a methyl group from lysine at position 20 of the histone.
    GO:0061188    negative regulation of chromatin silencing at rDNA    Any process that decreases the rate, frequency, or extent of the repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0045943    positive regulation of transcription from RNA polymerase I promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase I 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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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: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.

 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
    FE2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3k3n)
 

(-) 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
  3k3n
    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
  PHF8_HUMAN | Q9UPP1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.11.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  300263
    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
  PHF8_HUMAN | Q9UPP1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PHF8_HUMAN | Q9UPP12wwu 3k3o 3kv4 4do0

(-) Related Entries Specified in the PDB File

3k3o