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- PDB-2n39: NMR solution structure of a C-terminal domain of the chromodomain... -

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Basic information

Entry
Database: PDB / ID: 2n39
TitleNMR solution structure of a C-terminal domain of the chromodomain helicase DNA-binding protein 1
ComponentsChromodomain-helicase-DNA-binding protein 1
KeywordsDNA BINDING PROTEIN / chromatin remodelling / CHD1 / C-terminal domain / nucleosomes
Function / homology
Function and homology information


nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / methylated histone binding / helicase activity / histone binding / DNA helicase / Estrogen-dependent gene expression / chromatin remodeling ...nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / methylated histone binding / helicase activity / histone binding / DNA helicase / Estrogen-dependent gene expression / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...CDH1/2, SANT-Helical linker 1 / CDH1/2 SANT-Helical linker 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / 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 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, Water refinement
AuthorsMohanty, B. / Silva, A.P.G. / Mackay, J.P. / Ryan, D.P.
CitationJournal: J. Mol. Biol. / Year: 2016
Title: The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain.
Authors: Mohanty, B. / Helder, S. / Silva, A.P. / Mackay, J.P. / Ryan, D.P.
History
DepositionMay 26, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromodomain-helicase-DNA-binding protein 1


Theoretical massNumber of molelcules
Total (without water)12,9051
Polymers12,9051
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 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Chromodomain-helicase-DNA-binding protein 1 / CHD-1 / ATP-dependent helicase CHD1


Mass: 12904.958 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 1409-1511)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1 / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: O14646

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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-13C HSQC aliphatic
1312D DQF-COSY
1412D 1H-1H TOCSY
1512D 1H-1H NOESY
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HNCO
1913D HN(CA)CO
11013D 1H-15N NOESY
11113D 1H-13C NOESY aliphatic
11213D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 440 uM [U-98% 13C; U-98% 15N] CHD1-C, 20 mM sodium phosphate, 10 mM NaCl, 1 mM DTT, 0.003 w/v sodium azide, 0.2 mM 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
440 uMCHD1-C-1[U-98% 13C; U-98% 15N]1
20 mMsodium phosphate-22
10 mMNaCl-33
1 mMDTT-44
0.003 w/vsodium azide-55
0.2 mM2,2-dimethyl-2-silapentane-5-sulfonate (DSS)-66
Sample conditionsIonic strength: 10 / pH: 6.5 / 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
TopSpin3.2Bruker Biospindata collection
TopSpin3.2Bruker Biospinprocessing
CARA1.5.3Keller and Wuthrichchemical shift assignment
CARA1.5.3Keller and Wuthrichpeak picking
UNIO2.0.1Herrmann and Wuthrichnoe assignment
UNIO2.0.1Herrmann and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
OPALp1.2Koradi,Billeter and Guntertwater refinement
CYANAGuntert, Mumenthaler and Wuthrichrefinement
OPALpKoradi,Billeter and Guntertrefinement
RefinementMethod: torsion angle dynamics, Water refinement / Software ordinal: 1
NMR constraintsNOE constraints total: 1335 / NOE intraresidue total count: 357 / NOE long range total count: 224 / NOE medium range total count: 388 / NOE sequential total count: 366
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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