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- PDB-2l11: Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide -

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Basic information

Entry
Database: PDB / ID: 2l11
TitleSolution NMR structure of the Cbx3 in complex with H3K9me3 peptide
Components
  • Chromobox protein homolog 3
  • Histone H3
KeywordsTRANSCRIPTION REGULATOR / chromodomain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


senescence-associated heterochromatin focus / chromatin lock complex / histone methyltransferase binding / condensed chromosome, centromeric region / nuclear inner membrane / : / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / cellular response to dexamethasone stimulus ...senescence-associated heterochromatin focus / chromatin lock complex / histone methyltransferase binding / condensed chromosome, centromeric region / nuclear inner membrane / : / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / cellular response to dexamethasone stimulus / pericentric heterochromatin / heterochromatin / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription coregulator binding / RNA Polymerase I Promoter Escape / euchromatin / RNA polymerase II transcription regulator complex / spindle / structural constituent of chromatin / rhythmic process / nuclear envelope / heterochromatin formation / nucleosome / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / protein domain specific binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromobox protein homologue 3 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain ...Chromobox protein homologue 3 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Histone H3.2 / Chromobox protein homolog 3 / Histone H3
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsKaustov, L. / Lemak, A. / Fares, C. / Gutmanas, A. / Quang, H. / Loppnau, P. / Min, J. / Edwards, A. / Arrowsmith, C. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Recognition and specificity determinants of the human cbx chromodomains.
Authors: Kaustov, L. / Ouyang, H. / Amaya, M. / Lemak, A. / Nady, N. / Duan, S. / Wasney, G.A. / Li, Z. / Vedadi, M. / Schapira, M. / Min, J. / Arrowsmith, C.H.
History
DepositionJul 22, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 4, 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: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Mar 26, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 3
B: Histone H3


Theoretical massNumber of molelcules
Total (without water)7,9622
Polymers7,9622
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 Chromobox protein homolog 3 / Heterochromatin protein 1 homolog gamma / HP1 gamma / Modifier 2 protein / HECH


Mass: 6354.091 Da / Num. of mol.: 1 / Fragment: UNP Residues 29-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon plus RIL / References: UniProt: Q13185
#2: Protein/peptide Histone H3


Mass: 1607.877 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-16 / Source method: obtained synthetically / Details: H3K9ME3 15-mer peptide / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133, UniProt: P84233*PLUS
Has protein modificationY

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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 CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D-15N-NOESY
1913D-13C-NOESY
11013D -13C-aromatic-NOESY
11113D (H)CCH-TOCSY
112113C/15N-filtered/edited NOESY
11313D aro 1H-13C NOESY
11413D-aromatic 1H-13C-TOCSY

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Sample preparation

DetailsContents: 20 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.5 mM PMSF, 1 mM Benzamidine, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate-11
200 mMsodium chloride-21
2 mMDTT-31
1 mMTCEP-41
0.5 mMPMSF-51
1 mMBenzamidine-61
Sample conditionsIonic strength: 200 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameDeveloperClassification
ABACUS(ABACUS)-Grishaevchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
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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