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- PDB-3i90: Crystal structure of human chromobox homolog 6 (CBX6) with H3K27 ... -

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Basic information

Entry
Database: PDB / ID: 3i90
TitleCrystal structure of human chromobox homolog 6 (CBX6) with H3K27 peptide
Components
  • Chromobox protein homolog 6
  • H3K27 peptide
KeywordsTRANSCRIPTION / chromobox homolog 6 / CBX6 / H3K27 peptide / Structural Genomics / Structural Genomics Consortium / SGC / Chromatin regulator / Nucleus / Phosphoprotein / Repressor / Transcription regulation
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 / methylated histone binding / Regulation of PTEN gene transcription / chromatin organization / Oxidative Stress Induced Senescence / single-stranded RNA binding / nuclear body ...PRC1 complex / PcG protein complex / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / heterochromatin / methylated histone binding / Regulation of PTEN gene transcription / chromatin organization / Oxidative Stress Induced Senescence / single-stranded RNA binding / nuclear body / 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 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 ...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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 6
B: Chromobox protein homolog 6
C: H3K27 peptide
D: H3K27 peptide


Theoretical massNumber of molelcules
Total (without water)14,7334
Polymers14,7334
Non-polymers00
Water1,17165
1
A: Chromobox protein homolog 6
C: H3K27 peptide


Theoretical massNumber of molelcules
Total (without water)7,3672
Polymers7,3672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-6.3 kcal/mol
Surface area4390 Å2
MethodPISA
2
B: Chromobox protein homolog 6
D: H3K27 peptide


Theoretical massNumber of molelcules
Total (without water)7,3672
Polymers7,3672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-5.5 kcal/mol
Surface area4080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.421, 53.421, 227.778
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Chromobox protein homolog 6


Mass: 6177.187 Da / Num. of mol.: 2 / Fragment: Chromo domain: UNP residues 9-64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: O95503
#2: Protein/peptide H3K27 peptide


Mass: 1189.428 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.5M (NH4)2SO4, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 13855 / % possible obs: 99.7 % / Redundancy: 17.1 % / Rmerge(I) obs: 0.1 / Χ2: 2.014 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.0819.30.6348861.554199.6
2.38-2.48190.5249061.615199.9
2.48-2.59190.4459001.7391100
2.59-2.7318.80.3279141.8571100
2.73-2.918.60.2349132.1251100
2.9-3.1218.20.1629302.5991100
3.12-3.4417.60.1119252.4871100
3.44-3.9316.90.0849492.4061100
3.93-4.95150.0639712.0421100
4.95-4010.20.05610821.644197.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GV6

3gv6


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.871 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.3 687 5 %RANDOM
Rwork0.252 ---
obs0.254 13855 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.8 Å2 / Biso mean: 21.237 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.69 Å20 Å2
2--1.39 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 0 65 1042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022995
X-RAY DIFFRACTIONr_angle_refined_deg1.9421.9581339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5545117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.81621.70741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.13415175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0511510
X-RAY DIFFRACTIONr_chiral_restr0.1540.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02714
X-RAY DIFFRACTIONr_mcbond_it0.9521.5598
X-RAY DIFFRACTIONr_mcangle_it1.5322943
X-RAY DIFFRACTIONr_scbond_it2.6383397
X-RAY DIFFRACTIONr_scangle_it3.7344.5396
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 53 -
Rwork0.437 877 -
all-930 -
obs--91.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.8418-1.25051.593410.3358-3.53558.38010.3092-0.2741-0.2426-0.1773-0.03020.31050.0818-0.1398-0.2790.1936-0.107-0.11480.2231-0.04190.1305-1.797117.956816.7552
27.57250.15011.9195.23930.656110.74680.2267-0.1024-0.1473-0.0155-0.07850.09680.0221-0.0648-0.14820.1713-0.0775-0.06070.18610.0080.1025-0.73317.550917.4194
39.09491.471.92348.04934.58689.866-0.01020.19140.0027-0.53090.2446-0.2087-0.55830.0422-0.23440.2793-0.0391-0.08870.1642-0.03420.1384-4.977319.650.5985
44.29782.76344.54916.47554.098512.2867-0.0342-0.14160.0757-0.39980.12920.2162-0.5056-0.2981-0.0950.30050.0079-0.03580.1442-0.04390.1454-6.94216.9861-1.2863
521.3251-1.68020.883211.72184.63711.2755-0.4482-0.007-0.18810.39170.4079-0.29160.46860.66250.04030.3128-0.0697-0.11710.30650.03880.16842.668210.581322.586
614.71148.80013.818521.464512.84316.62080.3126-0.237-0.5739-0.68340.7216-1.4483-0.49061.7507-1.03420.6296-0.1381-0.07141.077-0.25530.1628-2.877513.381-8.9164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 22
2X-RAY DIFFRACTION2A23 - 58
3X-RAY DIFFRACTION3B10 - 36
4X-RAY DIFFRACTION4B37 - 59
5X-RAY DIFFRACTION5C19 - 29
6X-RAY DIFFRACTION6D19 - 28

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