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- PDB-3gv6: Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 p... -

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Basic information

Entry
Database: PDB / ID: 3gv6
TitleCrystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
Components
  • Chromobox protein homolog 6
  • Histone H3K9me3 peptide
KeywordsTranscription/DNA binding protein / chromobox homolog / CBX6 / H3K9 peptide / SGC / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription / Transcription regulation / Chromosomal protein / DNA-binding / Nucleosome core / Transcription-DNA binding protein COMPLEX / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


PRC1 complex / PcG protein complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / : / heterochromatin / Regulation of PTEN gene transcription / structural constituent of chromatin / nucleosome / chromatin organization / Oxidative Stress Induced Senescence ...PRC1 complex / PcG protein complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / : / heterochromatin / Regulation of PTEN gene transcription / structural constituent of chromatin / nucleosome / chromatin organization / Oxidative Stress Induced Senescence / single-stranded RNA binding / nuclear body / protein heterodimerization activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
: / 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 ...: / 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 / 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
Chromobox protein homolog 6 / Histone H3.2 / Histone H3
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsDong, A. / Amaya, M.F. / Li, Z. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. ...Dong, A. / Amaya, M.F. / Li, Z. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Ouyang, H. / 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
DepositionMar 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromobox protein homolog 6
B: Histone H3K9me3 peptide


Theoretical massNumber of molelcules
Total (without water)8,7452
Polymers8,7452
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-5 kcal/mol
Surface area4280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.075, 40.454, 53.376
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chromobox protein homolog 6


Mass: 7137.208 Da / Num. of mol.: 1 / Fragment: UNP residues 8-65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX6 / Plasmid: P28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95503
#2: Protein/peptide Histone H3K9me3 peptide


Mass: 1607.877 Da / Num. of mol.: 1 / Fragment: UNP residues 2-16 / Source method: obtained synthetically / Details: This sequence occurs naturally in Xenopus laevis / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133, UniProt: P84233*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 29.03 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 14% PEG 3350, 0.2M MgCl2, 0.1M HEPES, pH7.5 , VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 3, 2009 / Details: VeriMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 6339 / Num. obs: 6339 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.66 / Num. unique all: 547 / Rsym value: 0.473 / % possible all: 89.2

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DM1

3dm1


Resolution: 1.76→24.85 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.142 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26634 437 6.9 %RANDOM
Rwork0.20988 ---
all0.21354 5870 --
obs0.21354 5870 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.219 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å20 Å20 Å2
2---0.69 Å20 Å2
3---2.55 Å2
Refinement stepCycle: LAST / Resolution: 1.76→24.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms521 0 0 49 570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022537
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.391.947723
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.914562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61121.48127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1611597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.723158
X-RAY DIFFRACTIONr_chiral_restr0.1160.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1870.2231
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2358
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8791.5327
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4182500
X-RAY DIFFRACTIONr_scbond_it1.9393254
X-RAY DIFFRACTIONr_scangle_it2.9994.5223
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 27 -
Rwork0.408 353 -
obs--86.17 %

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