Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE TUDOR DOMAIN OF METAL-RESPONSE ELEMENT-BINDING TRANSCRIPTION FACTOR 2
 
Authors :  W. Dang, Y. Muto, K. Isono, S. Watanabe, T. Tarada, T. Kigawa, H. Koseki, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Nmr, Structure Genomics, Tudor Domain, Metal-Response Element- Binding Transcription Factor 2, Zinc-Regulated Factor 1, Zirf1, Metal-Response Element Dna-Binding Protein M96, Metal-Regulatory Transcription Factor 2, Pcl2, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Dang, Y. Muto, K. Isono, S. Watanabe, T. Tarada, T. Kigawa, H. Koseki, S. Yokoyama
Solution Structure Of The Tudor Domain Of Metal-Response Element-Binding Transcription Factor 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METAL-RESPONSE ELEMENT-BINDING TRANSCRIPTION FACTOR 2
    ChainsA
    EngineeredYES
    Expression System PlasmidP061002-01
    Expression System Vector TypePLASMID
    FragmentTUDOR DOMAIN
    GeneMTF2
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymZINC-REGULATED FACTOR 1, ZIRF1, METAL-RESPONSE ELEMENT DNA-BINDING PROTEIN M96, METAL-REGULATORY TRANSCRIPTION FACTOR 2, PCL2

 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 2EQJ)

(-) Sites  (0, 0)

(no "Site" information available for 2EQJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EQJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2EQJ)

(-) 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:66
 aligned with MTF2_MOUSE | Q02395 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:91
                                    17        27        37        47        57        67        77        87        97 
            MTF2_MOUSE    8 GNSLVHKRSPLRRNQKTSASLNKLSLQDGHKAKKPACKFEEGQDVLARWSDGLFYLGTIKKINILKQSCFIIFEDSSKSWVLWKDIQTGAT 98
               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) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  2eqj A  1 GSS-------------------------GSSGKKPACKFEEGQDVLARWSDGLFYLGTIKKINILKQSCFIIFEDSSKSWVLWKDIQTGAT 66
                              |      -         -        |5        15        25        35        45        55        65 
                              3                         4                                                              

   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 2EQJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

NMR Structure(hide GO term definitions)
Chain A   (MTF2_MOUSE | Q02395)
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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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: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: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:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0007379    segment specification    The process in which segments assume individual identities; exemplified in insects by the actions of the products of the homeotic genes.
    GO:0048863    stem cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:0019827    stem cell population maintenance    The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types.
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: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

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 2eqj)
 
  Sites
(no "Sites" information available for 2eqj)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2eqj)
 

(-) 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
  2eqj
    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
  MTF2_MOUSE | Q02395
    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
  MTF2_MOUSE | Q02395
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MTF2_MOUSE | Q023952yt5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2EQJ)