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- PDB-2k1b: Solution NMR structure of the chromo domain of the chromobox prot... -

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Basic information

Entry
Database: PDB / ID: 2k1b
TitleSolution NMR structure of the chromo domain of the chromobox protein homolog 7
ComponentsChromobox protein homolog 7
KeywordsTRANSCRIPTION REGULATOR / alpha/beta protein / Chromatin regulator / Nucleus / Repressor / Transcription / Transcription regulation / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


PRC1 complex / PcG protein complex / chromatin organization / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Chromobox protein homolog 7 / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / 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 ...Chromobox protein homolog 7 / CBX family C-terminal motif / CBX family C-terminal motif / Chromo domain subgroup / 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 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chromobox protein homolog 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsKaustov, L. / Lemak, A. / Quyang, H. / Gutmanas, A. / Fares, C. / Bountra, C. / Weigelt, J. / Loppnau, P. / Ravichandran, M. / Edwards, A.M. ...Kaustov, L. / Lemak, A. / Quyang, H. / Gutmanas, A. / Fares, C. / Bountra, C. / Weigelt, J. / Loppnau, P. / Ravichandran, M. / Edwards, A.M. / Min, J. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Solution NMR structure of the chromobox protein homolog 7.
Authors: Kaustov, L. / Lemak, A. / Quyang, H. / Gutmanas, A. / Fares, C. / Bountra, C. / Weigelt, J. / Loppnau, P. / Ravichandran, M. / Edwards, A.M. / Min, J. / Arrowsmith, C.H.
History
DepositionFeb 25, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 7


Theoretical massNumber of molelcules
Total (without water)8,9601
Polymers8,9601
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromobox protein homolog 7


Mass: 8960.181 Da / Num. of mol.: 1 / Fragment: Chromo domain: Residues 7-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX7 / Plasmid: pET28a-mhl / Production host: Escherichia coli (E. coli) / References: UniProt: O95931

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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
1313D HNCO
1413D HBHA(CO)NH
1513D CBCA(CO)NH
1613D HNCA
1713D (H)CCH-TOCSY
1813D (H)CCH-TOCSY
1913D 1H-13C NOESY
11013D 1H-15N NOESY
11113D aromat 1H-13C NOESY

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Sample preparation

DetailsContents: 10 mM phosphate, 300 mM sodium chloride, 2 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 mMphosphate1
300 mMsodium chloride1
2 mMDTT1
Sample conditionsIonic strength: 300 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameDeveloperClassification
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANADelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxrefinement
RefinementMethod: molecular dynamics / 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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