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- PDB-2ckc: Solution structures of the BRK domains of the human Chromo Helica... -

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Basic information

Entry
Database: PDB / ID: 2ckc
TitleSolution 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
ComponentsCHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 7
KeywordsHYDROLASE / PROTEIN-PROTEIN INTERACTION / PHOSPHORYLATION / DISEASE MUTATION / NUCLEOTIDE-BINDING / TRANSCRIPTION REGULATION / TRANSCRIPTION ELONGATION / CHROMATIN REGULATOR / CHROMATIN REMODELING / HELICASE / BRK DOMAIN / ATP-BINDING / DNA-BINDING / TRANSCRIPTION / NUCLEAR PROTEIN
Function / homology
Function and homology information


right ventricular compact myocardium morphogenesis / semicircular canal morphogenesis / nose development / regulation of growth hormone secretion / epithelium development / female genitalia development / cranial nerve development / olfactory nerve development / aorta morphogenesis / olfactory behavior ...right ventricular compact myocardium morphogenesis / semicircular canal morphogenesis / nose development / regulation of growth hormone secretion / epithelium development / female genitalia development / cranial nerve development / olfactory nerve development / aorta morphogenesis / olfactory behavior / secondary palate development / genitalia development / atrioventricular canal development / chordate embryonic development / olfactory bulb development / innervation / ventricular trabecula myocardium morphogenesis / positive regulation of multicellular organism growth / adult heart development / adult walking behavior / blood circulation / embryonic hindlimb morphogenesis / ATP-dependent chromatin remodeler activity / limb development / inner ear morphogenesis / cardiac septum morphogenesis / face development / T cell differentiation / regulation of neurogenesis / blood vessel remodeling / heart morphogenesis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / helicase activity / skeletal system development / central nervous system development / promoter-specific chromatin binding / sensory perception of sound / response to bacterium / cognition / rRNA processing / retina development in camera-type eye / histone binding / regulation of gene expression / DNA helicase / in utero embryonic development / transcription by RNA polymerase II / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Ribosomal Protein L9; domain 1 - #120 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Ribosomal Protein L9; domain 1 / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : ...Ribosomal Protein L9; domain 1 - #120 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Ribosomal Protein L9; domain 1 / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CANDID IN CYANA
AuthorsAb, E. / de Jong, R.N. / Diercks, T. / Xiaoyun, J. / Daniels, M. / Kaptein, R. / Folkers, G.E.
CitationJournal: To be Published
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: Ab, E. / De Jong, R.N. / Diercks, T. / Xiaoyun, J. / Daniels, M. / Kaptein, R. / Folkers, G.E.
History
DepositionApr 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 7


Theoretical massNumber of molelcules
Total (without water)9,0811
Polymers9,0811
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 7 / ATP-DEPENDENT HELICASE CHD7 / CHD-7


Mass: 9081.252 Da / Num. of mol.: 1 / Fragment: BRK, RESIDUES 1801-1860
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: SELF MADE CDNA LIBRARY OF MULTIPLE HUMAN CARCINOMA CELL LINES
Plasmid: PHISLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q9P2D1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HN(CA)CO
131HN(CA)CB
141CBCA(CO)NH
151HBHA(CO)NH
161HNCAHA
171C(CO)NH
181CCH-COSY
191(H)CCH- TOCSY
1101HNH-NOESY
1111HCH- NOESY
1121CNH-NOESY
1131HH- NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED HIS-TAGGED CHROMODOMAIN HELICASE DNA BINDING PROTEIN 7 2564-2622

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Sample preparation

DetailsContents: 5% D2O/95% H2O
Sample conditionsIonic strength: 150 mM / pH: 6.0 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
RefinementMethod: CANDID IN CYANA / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 25

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