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- PDB-2dl6: Solution structure of the first BRK domain from human chromodomai... -

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Basic information

Entry
Database: PDB / ID: 2dl6
TitleSolution structure of the first BRK domain from human chromodomain-helicase-DNA-binding protein 8
ComponentsChromodomain-helicase-DNA-binding protein 8
KeywordsGENE REGULATION / BRK / CHD8 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


digestive tract development / negative regulation of fibroblast apoptotic process / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase III / social behavior / MLL1 complex / prepulse inhibition / methylated histone binding / DNA helicase activity / Deactivation of the beta-catenin transactivating complex ...digestive tract development / negative regulation of fibroblast apoptotic process / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase III / social behavior / MLL1 complex / prepulse inhibition / methylated histone binding / DNA helicase activity / Deactivation of the beta-catenin transactivating complex / brain development / negative regulation of canonical Wnt signaling pathway / mRNA processing / beta-catenin binding / Wnt signaling pathway / p53 binding / histone binding / DNA helicase / in utero embryonic development / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Chromodomain-helicase-DNA-binding protein 8 / 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 ...Chromodomain-helicase-DNA-binding protein 8 / 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 / 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
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSuetake, T. / Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the first BRK domain from human chromodomain-helicase-DNA-binding protein 8
Authors: Suetake, T. / Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionApr 17, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromodomain-helicase-DNA-binding protein 8


Theoretical massNumber of molelcules
Total (without water)9,3201
Polymers9,3201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violation, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromodomain-helicase-DNA-binding protein 8 / ATP-dependent helicase CHD8 / CHD-8 / Helicase with SNF2 domain 1


Mass: 9320.400 Da / Num. of mol.: 1 / Fragment: BRK domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: CHD8, KIAA1564 / Plasmid: P051017-15 / Production host: Cell free synthesis / References: UniProt: Q9HCK8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.01mM 13C, 15N-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVARIANcollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9321Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violation, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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