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 STRUCTURES OF THE BRK DOMAINS OF THE HUMAN CHROMO HELICASE DOMAIN 7 AND 8, REVEALS STRUCTURAL SIMILARITY WITH GYF DOMAIN SUGGESTING A ROLE IN PROTEIN INTERACTION
 
Authors :  E. Ab, R. N. De Jong, T. Diercks, J. Xiaoyun, M. Daniels, R. Kaptein, G. E. Folkers
Date :  14 Apr 06  (Deposition) - 08 May 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Brk Domain, Transcription Elongation, Chromatin Remodeling, Protein-Protein Interaction, Transcription, Hydrolase, Helicase, Nuclear Protein, Chromatin Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Ab, R. N. De Jong, T. Diercks, J. Xiaoyun, M. Daniels, R. Kaptein, G. E. Folkers
Solution Structures Of The Brk Domains Of The Human Chromo Helicase Domain 7 And 8, Reveals Structural Similarity With Gyf Domain Suggesting A Role In Protein Interaction
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 8
    ChainsA
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHISLIC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA
    FragmentBRK DOMAIN, RESIDUES 2012-2085
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSELF MADE CDNA LIBRARY OF MULTIPLE HUMAN CARCINOMA CELL LINES
    SynonymATP-DEPENDENT HELICASE CHD8, CHD-8, HELICASE WITH SNF2 DOMAIN 1

 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 2CKA)

(-) Sites  (0, 0)

(no "Site" information available for 2CKA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3ENST000003999823ENSE00001541186chr14:21899397-21898960438CHD8_HUMAN1-1461460--
1.5ENST000003999825ENSE00001424069chr14:21897494-21897123372CHD8_HUMAN147-2701240--
1.6ENST000003999826ENSE00001422532chr14:21896413-21896028386CHD8_HUMAN271-3991290--
1.7ENST000003999827ENSE00001418360chr14:21894401-21894287115CHD8_HUMAN399-437390--
1.8ENST000003999828ENSE00000653248chr14:21884066-21883884183CHD8_HUMAN438-498610--
1.9ENST000003999829ENSE00000653240chr14:21883801-2188373369CHD8_HUMAN499-521230--
1.10ENST0000039998210ENSE00000653233chr14:21883152-2188309756CHD8_HUMAN522-540190--
1.11ENST0000039998211ENSE00000653232chr14:21882577-21882460118CHD8_HUMAN540-579400--
1.12ENST0000039998212ENSE00000940587chr14:21881155-2188107284CHD8_HUMAN580-607280--
1.13ENST0000039998213ENSE00000930049chr14:21878147-21878010138CHD8_HUMAN608-653460--
1.14ENST0000039998214ENSE00000889099chr14:21876984-21876863122CHD8_HUMAN654-694410--
1.15ENST0000039998215ENSE00000889098chr14:21876714-21876471244CHD8_HUMAN694-775820--
1.16ENST0000039998216ENSE00000889097chr14:21875191-21875015177CHD8_HUMAN776-834590--
1.17ENST0000039998217ENSE00001673287chr14:21874023-21873880144CHD8_HUMAN835-882480--
1.18ENST0000039998218ENSE00001737016chr14:21873623-21873368256CHD8_HUMAN883-968860--
1.19ENST0000039998219ENSE00001207501chr14:21871822-21871612211CHD8_HUMAN968-1038710--
1.20ENST0000039998220ENSE00001739488chr14:21871371-21871176196CHD8_HUMAN1038-1103660--
1.21ENST0000039998221ENSE00000653225chr14:21870662-21870495168CHD8_HUMAN1104-1159560--
1.22ENST0000039998222ENSE00000653224chr14:21870295-21870116180CHD8_HUMAN1160-1219600--
1.23ENST0000039998223ENSE00001207619chr14:21869672-21869562111CHD8_HUMAN1220-1256370--
1.24ENST0000039998224ENSE00000653222chr14:21869230-21869034197CHD8_HUMAN1257-1322660--
1.25ENST0000039998225ENSE00000889094chr14:21868771-21868572200CHD8_HUMAN1322-1389680--
1.26ENST0000039998226ENSE00000889093chr14:21868466-21868310157CHD8_HUMAN1389-1441530--
1.27ENST0000039998227ENSE00000653219chr14:21868229-2186814090CHD8_HUMAN1441-1471310--
1.28ENST0000039998228ENSE00000653218chr14:21867864-21867761104CHD8_HUMAN1471-1506360--
1.29ENST0000039998229ENSE00000653217chr14:21866111-21865982130CHD8_HUMAN1506-1549440--
1.30ENST0000039998230ENSE00000653216chr14:21864051-2186397676CHD8_HUMAN1549-1574260--
1.31ENST0000039998231ENSE00000889092chr14:21863511-2186345755CHD8_HUMAN1575-1593190--
1.32ENST0000039998232ENSE00000889091chr14:21863278-21863071208CHD8_HUMAN1593-1662700--
1.33ENST0000039998233ENSE00001096837chr14:21862644-21862436209CHD8_HUMAN1662-1732710--
1.34ENST0000039998234ENSE00001096842chr14:21862354-21861635720CHD8_HUMAN1732-19722410--
1.35ENST0000039998235ENSE00001096834chr14:21861413-21861265149CHD8_HUMAN1972-2021500--
1.36ENST0000039998236ENSE00001096823chr14:21860968-21860666303CHD8_HUMAN2022-21221010--
1.37ENST0000039998237ENSE00001096825chr14:21860105-21859992114CHD8_HUMAN2123-2160380--
1.38ENST0000039998238ENSE00001096832chr14:21859801-21859622180CHD8_HUMAN2161-2220600--
1.39ENST0000039998239ENSE00001096840chr14:21859222-21859106117CHD8_HUMAN2221-2259390--
1.40ENST0000039998240ENSE00001096848chr14:21854335-21853358978CHD8_HUMAN2260-24461871A:2028-208558

(-) 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:58
 aligned with CHD8_HUMAN | Q9HCK8 from UniProtKB/Swiss-Prot  Length:2581

    Alignment length:58
                                  2316      2326      2336      2346      2356        
          CHD8_HUMAN   2307 LDVDLETRIPVINKVDGTLLVGEDAPRRAELEMWLQGHPEFAVDPRFLAYMEDRRKQK 2364
               SCOP domains d2ckaa1 A:2028-2085                                        SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.....ee......hhhhhhhhhhhh..eeehhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.40  PDB: A:2028-2085 UniProt: 2260-2446             Transcript 1
                2cka A 2028 LDVDLETRIPVINKVDGTLLVGEDAPRRAELEMWLQGHPEFAVDPRFLAYMEDRRKQK 2085
                                  2037      2047      2057      2067      2077        

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 37)

NMR Structure(hide GO term definitions)
Chain A   (CHD8_HUMAN | Q9HCK8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    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:0070016    armadillo repeat domain binding    Interacting selectively and non-covalently with the armadillo repeat domain of a protein, an approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity protein armadillo. Arm-repeat proteins are involved in various processes, including intracellular signalling and cytoskeletal regulation.
    GO:0008013    beta-catenin binding    Interacting selectively and non-covalently with the beta subunit of the catenin complex.
    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:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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: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: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: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:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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).
biological process
    GO:0043044    ATP-dependent chromatin remodeling    Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
    GO:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    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:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0048565    digestive tract development    The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0030178    negative regulation of Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:2000270    negative regulation of fibroblast apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast apoptotic process.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    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:0045945    positive regulation of transcription from RNA polymerase III promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase III 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:0071339    MLL1 complex    A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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

(-) 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
  2cka
    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
  CHD8_HUMAN | Q9HCK8
    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
  CHD8_HUMAN | Q9HCK8
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CHD8_HUMAN | Q9HCK82dl6

(-) Related Entries Specified in the PDB File

2dl6 SOLUTION STRUCTURE OF THE FIRST BRK DOMAIN FROM HUMANCHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 8