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- PDB-2kvm: Solution structure of the CBX7 chromodomain in complex with a H3K... -

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Basic information

Entry
Database: PDB / ID: 2kvm
TitleSolution structure of the CBX7 chromodomain in complex with a H3K27me2 peptide
Components
  • Chromobox protein homolog 7
  • histone H3 peptide (residues 15-30) with dimethylated lysine 27
KeywordsTRANSCRIPTION / histone modification / lysine methylation / chromobox / polycomb / chromatin-binding / Chromatin regulator / Nucleus / Repressor / Transcription regulation
Function / homology
Function and homology information


sebaceous gland development / PRC1 complex / PcG protein complex / heterochromatin / methylated histone binding / positive regulation of transcription elongation by RNA polymerase II / chromatin organization / single-stranded RNA binding / chromatin binding / nucleus
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 speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsYap, K.L. / Zeng, L. / Zhou, M.
CitationJournal: Mol.Cell / Year: 2010
Title: Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a.
Authors: Yap, K.L. / Li, S. / Munoz-Cabello, A.M. / Raguz, S. / Zeng, L. / Mujtaba, S. / Gil, J. / Walsh, M.J. / Zhou, M.M.
History
DepositionMar 17, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 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 / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model ..._pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromobox protein homolog 7
B: histone H3 peptide (residues 15-30) with dimethylated lysine 27


Theoretical massNumber of molelcules
Total (without water)10,5642
Polymers10,5642
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Chromobox protein homolog 7


Mass: 8838.141 Da / Num. of mol.: 1 / Fragment: chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cbx7, D15Ertd417e / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VDS3
#2: Protein/peptide histone H3 peptide (residues 15-30) with dimethylated lysine 27


Mass: 1726.075 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
2222D 1H-13C HSQC
3332D 1H-1H TOCSY
2423D HN(CA)CB
2523D HN(COCA)CB
1613D 1H-15N NOESY
2723D 1H-13C NOESY
2823D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 15N] CBX7 chromodomain, 0.75 mM H3K27me2 peptide, 4.3 mM sodium phosphate, 1.4 mM potassium phosphate, 5 mM DTT, 137 mM sodium chloride, 3 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-100% 13C; U-100% 15N] CBX7 chromodomain, 0.75 mM H3K27me2 peptide, 4.3 mM sodium phosphate, 1.4 mM potassium phosphate, 5 mM DTT, 137 mM sodium chloride, 3 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
30.5 mM H3K27me2 peptide, 4.3 mM sodium phosphate, 1.4 mM potassium phosphate, 5 mM DTT, 137 mM sodium chloride, 3 mM potassium chloride, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCBX7 chromodomain[U-100% 15N]1
0.75 mMH3K27me2 peptide1
4.3 mMsodium phosphate1
1.4 mMpotassium phosphate1
5 mMDTT1
137 mMsodium chloride1
3 mMpotassium chloride1
0.5 mMCBX7 chromodomain[U-100% 13C; U-100% 15N]2
0.75 mMH3K27me2 peptide2
4.3 mMsodium phosphate2
1.4 mMpotassium phosphate2
5 mMDTT2
137 mMsodium chloride2
3 mMpotassium chloride2
0.5 mMH3K27me2 peptide3
4.3 mMsodium phosphate3
1.4 mMpotassium phosphate3
5 mMDTT3
137 mMsodium chloride3
3 mMpotassium chloride3
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
11407.4ambient 298 K
21407.4ambient 298 K
31407.4ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AvanceBrukerAVANCE8002
Bruker DRXBrukerDRX6003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2Linge, O'Donoghue and Nilgeschemical shift assignment
ARIA2Linge, O'Donoghue and Nilgesstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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