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- PDB-3h91: Crystal structure of the complex of human chromobox homolog 2 (CB... -

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Basic information

Entry
Database: PDB / ID: 3h91
TitleCrystal structure of the complex of human chromobox homolog 2 (CBX2) and H3K27 peptide
Components
  • Chromobox protein homolog 2
  • H3K27 peptide
KeywordsTRANSCRIPTION / human chromobox homolog 2 / CBX2 / H3K27 / Structural Genomics / Structural Genomics Consortium / SGC / Chromatin regulator / DNA-binding / Nucleus / Repressor / Transcription regulation
Function / homology
Function and homology information


development of primary sexual characteristics / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / histone H3K9me2/3 reader activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / : / SUMOylation of DNA damage response and repair proteins / heterochromatin ...development of primary sexual characteristics / PRC1 complex / PcG protein complex / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / histone H3K9me2/3 reader activity / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / : / SUMOylation of DNA damage response and repair proteins / heterochromatin / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / euchromatin / structural constituent of chromatin / nucleosome / Oxidative Stress Induced Senescence / cell differentiation / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Chromobox protein homolog 2 / 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 ...Chromobox protein homolog 2 / 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 / 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 2 / Histone H3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
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

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 2
B: Chromobox protein homolog 2
C: H3K27 peptide
D: H3K27 peptide


Theoretical massNumber of molelcules
Total (without water)16,0554
Polymers16,0554
Non-polymers00
Water2,738152
1
A: Chromobox protein homolog 2
C: H3K27 peptide

A: Chromobox protein homolog 2
C: H3K27 peptide


Theoretical massNumber of molelcules
Total (without water)16,0554
Polymers16,0554
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4320 Å2
ΔGint-22 kcal/mol
Surface area7340 Å2
MethodPISA
2
A: Chromobox protein homolog 2
C: H3K27 peptide


Theoretical massNumber of molelcules
Total (without water)8,0272
Polymers8,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-5 kcal/mol
Surface area4370 Å2
MethodPISA
3
B: Chromobox protein homolog 2
D: H3K27 peptide

B: Chromobox protein homolog 2
D: H3K27 peptide


Theoretical massNumber of molelcules
Total (without water)16,0554
Polymers16,0554
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4410 Å2
ΔGint-22 kcal/mol
Surface area7320 Å2
MethodPISA
4
B: Chromobox protein homolog 2
D: H3K27 peptide


Theoretical massNumber of molelcules
Total (without water)8,0272
Polymers8,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-5 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.145, 84.013, 65.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Chromobox protein homolog 2


Mass: 6511.553 Da / Num. of mol.: 2 / Fragment: UNP residues 9-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14781
#2: Protein/peptide H3K27 peptide


Mass: 1515.776 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: Q92133*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG3350, 0.1 M Tris, pH8.5, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorDate: Jan 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 26030 / % possible obs: 93.8 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 38.995
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.2-1.243.30.69561.7
1.24-1.294.20.73181.9
1.29-1.355.80.70895.6
1.35-1.427.80.52999.3
1.42-1.519.10.364100
1.51-1.639.40.216100
1.63-1.799.60.118100
1.79-2.059.80.07100
2.05-2.599.90.042100
2.59-509.50.02299.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.204 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22299 1294 5 %RANDOM
Rwork0.20945 ---
obs0.21015 24729 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.163 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20 Å20 Å2
2---0.6 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 0 152 1166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221080
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9781460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.63422.60946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00115204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8361510
X-RAY DIFFRACTIONr_chiral_restr0.130.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02790
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.2420
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2725
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3350.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0891.5659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67321027
X-RAY DIFFRACTIONr_scbond_it2.4433492
X-RAY DIFFRACTIONr_scangle_it3.4184.5433
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 100 -
Rwork0.226 1808 -
obs--100 %

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