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- PDB-3tzd: Crystal structure of the complex of Human Chromobox Homolog 3 (CBX3) -

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Basic information

Entry
Database: PDB / ID: 3tzd
TitleCrystal structure of the complex of Human Chromobox Homolog 3 (CBX3)
Components
  • Chromobox protein homolog 3
  • Histone H1.4
KeywordsTRANSCRIPTION/DNA binding Protein / STRUCTURAL GENOMICS CONSORTIUM / SGC / CHROMATIN REGULATOR / NUCLEUS / PHOSPHOPROTEIN / REPRESSOR / TRANSCRIPTION REGULATION / TRANSCRIPTION-DNA binding Protein complex
Function / homology
Function and homology information


chromatin lock complex / histone methyltransferase binding / negative regulation of DNA recombination / condensed chromosome, centromeric region / Apoptosis induced DNA fragmentation / chromosome condensation / nucleosomal DNA binding / nuclear inner membrane / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Transcriptional Regulation by E2F6 ...chromatin lock complex / histone methyltransferase binding / negative regulation of DNA recombination / condensed chromosome, centromeric region / Apoptosis induced DNA fragmentation / chromosome condensation / nucleosomal DNA binding / nuclear inner membrane / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / heterochromatin formation / methylated histone binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription coregulator binding / RNA Polymerase I Promoter Escape / euchromatin / chromatin DNA binding / spindle / nucleosome assembly / structural constituent of chromatin / RNA polymerase II transcription regulator complex / histone deacetylase binding / rhythmic process / nucleosome / nuclear envelope / chromatin organization / double-stranded DNA binding / chromosome, telomeric region / chromatin remodeling / protein domain specific binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / RNA 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 / Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 ...Chromobox protein homologue 3 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Histone H1.4 / Chromobox protein homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 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: Plos One / Year: 2012
Title: Structural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a.
Authors: Ruan, J. / Ouyang, H. / Amaya, M.F. / Ravichandran, M. / Loppnau, P. / Min, J. / Zang, J.
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromobox protein homolog 3
T: Histone H1.4


Theoretical massNumber of molelcules
Total (without water)8,9862
Polymers8,9862
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-7 kcal/mol
Surface area4900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.209, 92.209, 92.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Chromobox protein homolog 3 / HECH / Heterochromatin protein 1 homolog gamma / HP1 gamma / Modifier 2 protein


Mass: 6905.726 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 / References: UniProt: Q13185
#2: Protein/peptide Histone H1.4 / Histone H1b


Mass: 2080.543 Da / Num. of mol.: 1 / Fragment: UNP residues 19-36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST1H1E, H1F4 / References: UniProt: P10412
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 3.64 Å3/Da / Density % sol: 66.16 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: peg, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 23, 2009 / Details: si
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→40 Å / Num. all: 12066 / Num. obs: 12066 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→29.16 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.968 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23115 575 4.8 %RANDOM
Rwork0.1987 ---
all0.20029 11460 --
obs0.20029 11460 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.509 Å2
Refinement stepCycle: LAST / Resolution: 1.81→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms579 0 0 79 658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022619
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.964833
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.798572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7482532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11415110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.478153
X-RAY DIFFRACTIONr_chiral_restr0.1190.285
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02470
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.2267
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2419
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3151.5380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7792583
X-RAY DIFFRACTIONr_scbond_it2.9393286
X-RAY DIFFRACTIONr_scangle_it4.2444.5250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.856 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 45 -
Rwork0.276 820 -
obs--100 %

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