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- PDB-3i91: Crystal structure of human chromobox homolog 8 (CBX8) with H3K9 p... -

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Basic information

Entry
Database: PDB / ID: 3i91
TitleCrystal structure of human chromobox homolog 8 (CBX8) with H3K9 peptide
Components
  • Chromobox protein homolog 8
  • H3K9 peptide
KeywordsTRANSCRIPTION / Chromobox homolog 8 / CBX8 / H3K9 peptide / Structural Genomics / Structural Genomics Consortium / SGC / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription regulation
Function / homology
Function and homology information


PRC1 complex / ubiquitin-protein transferase activator activity / histone H3K27me3 reader activity / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / : / positive regulation of collagen biosynthetic process / SUMOylation of DNA damage response and repair proteins ...PRC1 complex / ubiquitin-protein transferase activator activity / histone H3K27me3 reader activity / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / : / positive regulation of collagen biosynthetic process / SUMOylation of DNA damage response and repair proteins / heterochromatin / SUMOylation of transcription cofactors / positive regulation of DNA repair / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / cellular response to hydrogen peroxide / Oxidative Stress Induced Senescence / single-stranded RNA binding / positive regulation of cell population proliferation / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / CBX family C-terminal motif / CBX family C-terminal motif / 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 ...: / CBX family C-terminal motif / CBX family C-terminal motif / 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 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsAmaya, M.F. / Ravichandran, M. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. ...Amaya, M.F. / Ravichandran, M. / 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
DepositionJul 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 8
B: Chromobox protein homolog 8
C: H3K9 peptide


Theoretical massNumber of molelcules
Total (without water)14,1133
Polymers14,1133
Non-polymers00
Water3,873215
1
A: Chromobox protein homolog 8
C: H3K9 peptide


Theoretical massNumber of molelcules
Total (without water)7,5032
Polymers7,5032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-6.4 kcal/mol
Surface area4120 Å2
MethodPISA
2
B: Chromobox protein homolog 8


Theoretical massNumber of molelcules
Total (without water)6,6111
Polymers6,6111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.307, 51.545, 77.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chromobox protein homolog 8 / Polycomb 3 homolog / Pc3 / hPc3 / Rectachrome 1


Mass: 6610.602 Da / Num. of mol.: 2 / Fragment: Chromo domain: UNP residues 8-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX8, PC3, RC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q9HC52
#2: Protein/peptide H3K9 peptide


Mass: 892.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
Details: Cryo-cooled first crystal and sagitally focusing second crystal
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 23019

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.415 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1180 5.1 %RANDOM
Rwork0.213 ---
obs0.215 23019 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 67.95 Å2 / Biso mean: 19.565 Å2 / Biso min: 6.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---0.75 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 0 215 1161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022965
X-RAY DIFFRACTIONr_angle_refined_deg2.5361.9531293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.38821.42949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65915181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9611514
X-RAY DIFFRACTIONr_chiral_restr0.1750.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02718
X-RAY DIFFRACTIONr_mcbond_it1.7061.5553
X-RAY DIFFRACTIONr_mcangle_it2.692873
X-RAY DIFFRACTIONr_scbond_it3.83412
X-RAY DIFFRACTIONr_scangle_it5.7564.5420
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 74 -
Rwork0.329 1359 -
all-1433 -
obs--86.27 %

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