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- PDB-2n5n: Structure of an N-terminal domain of CHD4 -

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Basic information

Entry
Database: PDB / ID: 2n5n
TitleStructure of an N-terminal domain of CHD4
ComponentsChromodomain-helicase-DNA-binding protein 4
KeywordsDNA BINDING PROTEIN / HMG-box-like domain / CHD4 / PAR-binding
Function / homology
Function and homology information


cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / NuRD complex / regulation of stem cell differentiation / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / site of DNA damage / RNA Polymerase I Transcription Initiation ...cerebellar granule cell to Purkinje cell synapse / terminal button organization / regulation of cell fate specification / NuRD complex / regulation of stem cell differentiation / NGF-stimulated transcription / ATP-dependent chromatin remodeler activity / regulation of synapse assembly / site of DNA damage / RNA Polymerase I Transcription Initiation / Regulation of TP53 Activity through Acetylation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / helicase activity / HDACs deacetylate histones / transcription coregulator binding / double-strand break repair via homologous recombination / histone deacetylase binding / RNA polymerase II transcription regulator complex / transcription corepressor activity / histone binding / DNA helicase / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / chromosome, telomeric region / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / cytoplasm
Similarity search - Function
CHD subfamily II, SANT-like domain / Domain of unknown function DUF1087 / CHD, C-terminal 2 / CHD, N-terminal / CHD subfamily II, SANT-like domain / CHD subfamily II, DUF1087 / CHDNT (NUC034) domain / CHDCT2 (NUC038) domain / Domain of Unknown Function (DUF1086) / DUF1087 ...CHD subfamily II, SANT-like domain / Domain of unknown function DUF1087 / CHD, C-terminal 2 / CHD, N-terminal / CHD subfamily II, SANT-like domain / CHD subfamily II, DUF1087 / CHDNT (NUC034) domain / CHDCT2 (NUC038) domain / Domain of Unknown Function (DUF1086) / DUF1087 / Chromo domain signature. / 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 / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Chromo-like domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helicase conserved C-terminal domain / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / 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 / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsSilva, A.P.G. / Mackay, J.P.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The N-terminal Region of Chromodomain Helicase DNA-binding Protein 4 (CHD4) Is Essential for Activity and Contains a High Mobility Group (HMG) Box-like-domain That Can Bind Poly(ADP-ribose).
Authors: Silva, A.P. / Ryan, D.P. / Galanty, Y. / Low, J.K. / Vandevenne, M. / Jackson, S.P. / Mackay, J.P.
History
DepositionJul 22, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromodomain-helicase-DNA-binding protein 4


Theoretical massNumber of molelcules
Total (without water)9,5701
Polymers9,5701
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromodomain-helicase-DNA-binding protein 4 / CHD-4 / ATP-dependent helicase CHD4 / Mi-2 autoantigen 218 kDa protein / Mi2-beta


Mass: 9569.843 Da / Num. of mol.: 1 / Fragment: UNP residues 145-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD4 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / References: UniProt: Q14839

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-1H TOCSY
1312D DQF-COSY
1413D CBCA(CO)NH
1513D HNCO
1612D 1H-13C HSQC
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D HNHA
11013D C(CO)NH
11112D 1H-13C HSQC
11213D (H)CCH-TOCSY
11313D H(CCO)NH

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Sample preparation

DetailsContents: 350 uM [U-100% 13C; U-100% 15N] CHD4, 20 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM DSS, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
350 uMCHD4-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
150 mMsodium chloride-31
0.2 mMDSS-41
Sample conditionsIonic strength: 230 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
CNSBrunger, A.T. et al.refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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