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- PDB-2ee1: Solution structures of the Chromo domain of human chromodomain he... -

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Basic information

Entry
Database: PDB / ID: 2ee1
TitleSolution structures of the Chromo domain of human chromodomain helicase-DNA-binding protein 4
ComponentsChromodomain helicase-DNA-binding protein 4
KeywordsSIGNALING PROTEIN / EC 3.6.1.- / ATP- dependent helicase CHD4 / CHD-4 / Mi-2 autoantigen 218 kDa protein / Mi2-beta / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / site of DNA damage ...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 / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / site of DNA damage / RNA Polymerase I Transcription Initiation / Regulation of TP53 Activity through Acetylation / helicase activity / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / transcription coregulator binding / HDACs deacetylate histones / 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. / : / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / 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 / Zinc finger, PHD-type / PHD zinc finger / Helicase conserved C-terminal domain / Zinc finger, FYVE/PHD-type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSato, M. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structures of the Chromo domain of human chromodomain helicase-DNA-binding protein 4
Authors: Sato, M. / Tochio, N. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)7,6891
Polymers7,6891
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 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 7688.500 Da / Num. of mol.: 1 / Fragment: Chromo domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: CHD4 / Plasmid: P060904-16
References: UniProt: Q14839, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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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: 1mM Chromo domain U-15N, 13C; 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: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView2.0.17Johnson, B.A.data analysis
KUJIRA0.932Kobayashi, 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 violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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