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 CHROMO DOMAIN 2 IN CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 6
 
Authors :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 Mar 07  (Deposition) - 02 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Chromo Domain, 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 :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Chromo Domain 2 In Chromodomain-Helicase-Dna-Binding Protein 6
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 6
    ChainsA
    EC Number3.6.1.-
    EngineeredYES
    Expression System PlasmidP060904-12
    Expression System Vector TypePLASMID
    FragmentCHROMO DOMAIN, UNP RESIDUES 371-431
    GeneCHD6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymATP- DEPENDENT HELICASE CHD6, CHD-6, RADIATION- INDUCED GENE B PROTEIN

 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 2EPB)

(-) Sites  (0, 0)

(no "Site" information available for 2EPB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.CHD6_HUMAN375-418  1A:375-418

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003732331aENSE00001387501chr20:40247133-40246979155CHD6_HUMAN-00--
1.4ENST000003732334ENSE00001356151chr20:40179999-4017994456CHD6_HUMAN1-11110--
1.5bENST000003732335bENSE00000662096chr20:40162209-40161689521CHD6_HUMAN12-1851740--
1.6bENST000003732336bENSE00000662095chr20:40143591-40143444148CHD6_HUMAN185-234500--
1.7ENST000003732337ENSE00000662094chr20:40141634-40141485150CHD6_HUMAN235-284501A:364-369 (gaps)12
1.8aENST000003732338aENSE00001356142chr20:40127997-4012793563CHD6_HUMAN285-305210--
1.9aENST000003732339aENSE00000844811chr20:40126866-4012680859CHD6_HUMAN306-325200--
1.9cENST000003732339cENSE00000844810chr20:40126141-40126024118CHD6_HUMAN325-364400--
1.10ENST0000037323310ENSE00000844809chr20:40122584-4012249887CHD6_HUMAN365-393291A:371-39323
1.11ENST0000037323311ENSE00000844808chr20:40122312-40122178135CHD6_HUMAN394-438451A:394-43138
1.12ENST0000037323312ENSE00000844807chr20:40120459-40120338122CHD6_HUMAN439-479410--
1.13ENST0000037323313ENSE00000844806chr20:40118661-40118418244CHD6_HUMAN479-560820--
1.14cENST0000037323314cENSE00001036699chr20:40117244-40117068177CHD6_HUMAN561-619590--
1.15ENST0000037323315ENSE00000844804chr20:40116448-40116305144CHD6_HUMAN620-667480--
1.16aENST0000037323316aENSE00001036671chr20:40113247-40112992256CHD6_HUMAN668-753860--
1.17ENST0000037323317ENSE00000844802chr20:40112159-40111949211CHD6_HUMAN753-823710--
1.19aENST0000037323319aENSE00001801027chr20:40102157-40101962196CHD6_HUMAN823-888660--
1.20ENST0000037323320ENSE00000844800chr20:40086068-40085904165CHD6_HUMAN889-943550--
1.21ENST0000037323321ENSE00000844799chr20:40084619-40084440180CHD6_HUMAN944-1003600--
1.22ENST0000037323322ENSE00000844798chr20:40083376-40083266111CHD6_HUMAN1004-1040370--
1.23ENST0000037323323ENSE00000844797chr20:40081582-40081380203CHD6_HUMAN1041-1108680--
1.24ENST0000037323324ENSE00000844796chr20:40080665-40080466200CHD6_HUMAN1108-1175680--
1.25ENST0000037323325ENSE00000844795chr20:40079745-40079586160CHD6_HUMAN1175-1228540--
1.26ENST0000037323326ENSE00000844794chr20:40076611-4007652290CHD6_HUMAN1228-1258310--
1.27ENST0000037323327ENSE00000844793chr20:40074408-40074305104CHD6_HUMAN1258-1293360--
1.28ENST0000037323328ENSE00001377264chr20:40068769-40068640130CHD6_HUMAN1293-1336440--
1.29aENST0000037323329aENSE00001355850chr20:40065974-4006591461CHD6_HUMAN1336-1356210--
1.30bENST0000037323330bENSE00000844790chr20:40054793-4005473361CHD6_HUMAN1357-1377210--
1.31ENST0000037323331ENSE00000844789chr20:40054034-40053818217CHD6_HUMAN1377-1449730--
1.32ENST0000037323332ENSE00000844788chr20:40052340-40052132209CHD6_HUMAN1449-1519710--
1.33ENST0000037323333ENSE00000844786chr20:40050719-400491481572CHD6_HUMAN1519-20435250--
1.34ENST0000037323334ENSE00000844784chr20:40045989-40045838152CHD6_HUMAN2043-2093510--
1.35ENST0000037323335ENSE00000844783chr20:40045434-40045228207CHD6_HUMAN2094-2162690--
1.36ENST0000037323336ENSE00000844781chr20:40044278-40043826453CHD6_HUMAN2163-23131510--
1.37bENST0000037323337bENSE00000844778chr20:40042155-40041964192CHD6_HUMAN2314-2377640--
1.38ENST0000037323338ENSE00001317121chr20:40040903-40040784120CHD6_HUMAN2378-2417400--
1.39bENST0000037323339bENSE00001459829chr20:40034129-400307413389CHD6_HUMAN2418-27152980--

(-) 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 CHD6_HUMAN | Q8TD26 from UniProtKB/Swiss-Prot  Length:2715

    Alignment length:165
                                   276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426     
           CHD6_HUMAN   267 GAGRTSALSASTLAWQAEEPPEDDANIIEKILASKTVQEVHPGEPPFDLELFYVKYRNFSYLHCKWATMEELEKDPRIAQKIKRFRNKQAQMKHIFTEPDEDLFNPDYVEVDRILEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDVDPAKVKEFESLQV 431
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------....------------------------------.-------------------------------------------------------------........eeeeeeeee......eeeeeeee....hhhhh.eee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------CHROMO_2  PDB: A:375-418 UniProt: 375-418   ------------- PROSITE
           Transcript 1 (1) Exon 1.7          Exon 1.8a  PDB: -    Exon 1.9a  PDB: -   ---------------------------------------Exon 1.10  PDB: A:371-393    Exon 1.11  PDB: A:394-431 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.9c  PDB: - UniProt: 325-364      ------------------------------------------------------------------- Transcript 1 (2)
                 2epb A 364 GS------SGSS------------------------------G-------------------------------------------------------------NPDYVEVDRILEVAHTKDAETGEEVTHYLVKWCSLPYEESTWELEEDVDPAKVKEFESLQV 431
                             |     367 |       -         -         -  |      -         -         -         -         -         -    |  376       386       396       406       416       426     
                             |    366  |                            370                                                           371                                                            
                           365       369                                                                                                                                                         

   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 2EPB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (CHD6_HUMAN | Q8TD26)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0001221    transcription cofactor binding    Interacting selectively and non-covalently with a transcription cofactor, any protein involved in regulation of transcription via protein-protein interactions with transcription factors and other transcription regulatory proteins. Cofactors do not bind DNA directly, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
biological process
    GO:0036091    positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress    Any process that increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is under oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    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:0005665    DNA-directed RNA polymerase II, core complex    RNA polymerase II, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces mRNAs, snoRNAs, and some of the snRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The largest subunit of RNA polymerase II contains an essential carboxyl-terminal domain (CTD) composed of a variable number of heptapeptide repeats (YSPTSPS). The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerases I and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
    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

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 2epb)
 
  Sites
(no "Sites" information available for 2epb)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2epb)
 

(-) 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
  2epb
    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
  CHD6_HUMAN | Q8TD26
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.1.-
    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
  CHD6_HUMAN | Q8TD26
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2EPB)

(-) Related Entries Specified in the PDB File

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