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- PDB-2dy8: Solution structure of the second chromodomain of yeast Chd1 -

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Basic information

Entry
Database: PDB / ID: 2dy8
TitleSolution structure of the second chromodomain of yeast Chd1
ComponentsChromo domain protein 1
KeywordsHYDROLASE / Chromatin remodeling
Function / homology
Function and homology information


nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / nucleosome organization / SLIK (SAGA-like) complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SAGA complex ...nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / nucleosome organization / SLIK (SAGA-like) complex / sister chromatid cohesion / ATP-dependent chromatin remodeler activity / SAGA complex / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus
Similarity search - Function
Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 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. ...Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 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. / : / 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 / Chromo-like domain superfamily / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chromo domain-containing protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsOkuda, M. / Nishimura, Y.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Polymorphism of Chromodomains in Chd1
Authors: Okuda, M. / Horikoshi, M. / Nishimura, Y.
History
DepositionSep 7, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromo domain protein 1


Theoretical massNumber of molelcules
Total (without water)8,2871
Polymers8,2871
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromo domain protein 1 / ATP-dependent helicase CHD1


Mass: 8287.120 Da / Num. of mol.: 1 / Fragment: chromodomain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CHD1/YER164W / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P32657, 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
1112D NOESY
1222D NOESY
1333D 15N-separated NOESY
1453D 13C-separated NOESY
153HNHA
163HNHB
174HN(CO)HB
184HNCG
194HN(CO)CG

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-0.5mM chromodomain; 20mM potassium phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
20.3-0.5mM chromodomain; 20mM potassium phosphate buffer; 100% D2O100% D2O
30.3-0.5mM chromodomain U-15N; 20mM potassium phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
40.3-0.5mM chromodomain U-13C,15N; 20mM potassium phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
50.3-0.5mM chromodomain U-13C,15N; 20mM potassium phosphate buffer; 100% D2O100% D2O
Sample conditionsIonic strength: 300mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameDeveloperClassification
XwinNMRcollection
NMRPipeDelaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.processing
NMRViewJohnson, B.A., Blevins, R.A.data analysis
X-PLORBrunger, A.T.structure solution
X-PLORBrunger, A.T.refinement
RefinementMethod: 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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