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- PDB-2v0f: BRK domain from human CHD7 -

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Basic information

Entry
Database: PDB / ID: 2v0f
TitleBRK domain from human CHD7
ComponentsCHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 7
KeywordsHYDROLASE / NUCLEOTIDE-BINDING / CHROMATIN REGULATOR / CHARGE SYNDROME / PHOSPHORYLATION / DISEASE MUTATION / TRANSCRIPTION REGULATION / CHD7 / HELICASE / BRK DOMAIN / ATP-BINDING / DNA-BINDING / TRANSCRIPTION / NUCLEAR PROTEIN
Function / homology
Function and homology information


right ventricular compact myocardium morphogenesis / nose development / semicircular canal morphogenesis / epithelium development / regulation of growth hormone secretion / female genitalia development / cranial nerve development / olfactory behavior / olfactory nerve development / aorta morphogenesis ...right ventricular compact myocardium morphogenesis / nose development / semicircular canal morphogenesis / epithelium development / regulation of growth hormone secretion / female genitalia development / cranial nerve development / olfactory behavior / olfactory nerve development / aorta morphogenesis / secondary palate development / genitalia development / atrioventricular canal development / chordate embryonic development / olfactory bulb development / ventricular trabecula myocardium morphogenesis / adult heart development / positive regulation of multicellular organism growth / ATP-dependent chromatin remodeler activity / embryonic hindlimb morphogenesis / innervation / limb development / blood circulation / adult walking behavior / inner ear morphogenesis / cardiac septum morphogenesis / face development / blood vessel remodeling / T cell differentiation / regulation of neurogenesis / heart morphogenesis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / central nervous system development / skeletal system development / response to bacterium / promoter-specific chromatin binding / sensory perception of sound / cognition / rRNA processing / retina development in camera-type eye / regulation of gene expression / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / forked DNA-dependent helicase activity / four-way junction helicase activity / DNA helicase / in utero embryonic development / histone binding / 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 / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
: / : / Chromodomain-helicase-DNA-binding protein 6-9, tri-helical / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...: / : / Chromodomain-helicase-DNA-binding protein 6-9, tri-helical / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / 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
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CNS
AuthorsAllen, M.D. / Religa, T.L. / Freund, S.M.V. / Bycroft, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Solution Structure of the Brk Domains from Chd7
Authors: Allen, M.D. / Religa, T.L. / Freund, S.M.V. / Bycroft, M.
History
DepositionMay 14, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)9,5611
Polymers9,5611
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)20 / 22NO RESTRAINT VIOLATION
RepresentativeModel #1

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Components

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


Mass: 9560.885 Da / Num. of mol.: 1 / Fragment: BRK DOMAIN, RESIDUES 1869-1953
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: Q9P2D1, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
Sequence detailsEAW86834 AND NP_060250 ARE TWO OTHER REFERENCES FOR THE SEQUENCE

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY

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Sample preparation

DetailsContents: 0% WATER/90% D2O
Sample conditionspH: 6.5 / Pressure: 298.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
TOPSPIN; NMRVIEW; AZARA; ANSIG; CNSCNSstructure solution
RefinementMethod: CNS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: NO RESTRAINT VIOLATION / Conformers calculated total number: 22 / Conformers submitted total number: 20

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