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- PDB-5t1i: CBX3 chromo shadow domain in complex with histone H3 peptide -

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Basic information

Entry
Database: PDB / ID: 5t1i
TitleCBX3 chromo shadow domain in complex with histone H3 peptide
Components
  • Chromobox protein homolog 3
  • Histone H3.1Histone H3
KeywordsTRANSCRIPTION / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


chromatin lock complex / histone methyltransferase binding / condensed chromosome, centromeric region / nuclear inner membrane / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin ...chromatin lock complex / histone methyltransferase binding / condensed chromosome, centromeric region / nuclear inner membrane / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin / heterochromatin formation / epigenetic regulation of gene expression / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / transcription coregulator binding / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / euchromatin / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / RNA polymerase II transcription regulator complex / rhythmic process / nucleosome / nuclear envelope / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / chromatin remodeling / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / 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 / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus
Similarity search - Function
Chromobox protein homologue 3 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromobox protein homologue 3 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain subgroup / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / Chromobox protein homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1.
Authors: Liu, Y. / Qin, S. / Lei, M. / Tempel, W. / Zhang, Y. / Loppnau, P. / Li, Y. / Min, J.
History
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Structure summary
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Mar 8, 2017Group: Database references
Revision 1.4Apr 19, 2017Group: Database references
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 3
B: Chromobox protein homolog 3
C: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,14315
Polymers17,1433
Non-polymers012
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-25 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.737, 34.971, 45.833
Angle α, β, γ (deg.)90.000, 93.320, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAuthors did not experimentally determine the biological unit, but assigned it homologously to PDB entry 1S4Z.

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Components

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


Mass: 7637.704 Da / Num. of mol.: 2 / Fragment: unp residues 110-176
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q13185
#2: Protein/peptide Histone H3.1 / Histone H3 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1867.186 Da / Num. of mol.: 1 / Fragment: unp residues 39-53 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.9 Å3/Da / Density % sol: 35.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2 M sodium chloride, 0.1 M Hepes, 5% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791829 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791829 Å / Relative weight: 1
ReflectionResolution: 1.6→45.76 Å / Num. obs: 16432 / % possible obs: 95.5 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Net I/σ(I): 14.5 / Num. measured all: 55600
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) all% possible all
1.6-1.632.30.86112495490.5240.6781.10365.8
8.77-45.762.80.02342.73181120.9980.0170.02994.4

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3kup

3kup


Resolution: 1.6→27.79 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.243 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.113
Details: geometry restraints for the acetyl proline and arginine amide residues were prepared with GRADE (global phasing, using csd MOGUL app). model geometry was analyzed with phenix.molprobity. ...Details: geometry restraints for the acetyl proline and arginine amide residues were prepared with GRADE (global phasing, using csd MOGUL app). model geometry was analyzed with phenix.molprobity. anisotropic displacement parameters were analyzed on the PARVATI server.
RfactorNum. reflection% reflectionSelection details
Rfree0.2392 1088 6.6 %thin shells (sftools)
Rwork0.194 ---
obs0.197 15332 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56.78 Å2 / Biso mean: 24.65 Å2 / Biso min: 12.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20.11 Å2
2--0.83 Å20 Å2
3----1.16 Å2
Refinement stepCycle: final / Resolution: 1.6→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 12 44 1210
Biso mean--20.95 25.57 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191222
X-RAY DIFFRACTIONr_bond_other_d0.0020.021147
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.9551662
X-RAY DIFFRACTIONr_angle_other_deg0.96232638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43723.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53115198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.748157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2179
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211398
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02281
X-RAY DIFFRACTIONr_mcbond_it0.7821.463618
X-RAY DIFFRACTIONr_mcbond_other0.7821.463618
X-RAY DIFFRACTIONr_mcangle_it1.2582.189771
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.334 872 -
obs--69.37 %
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)
14.23560.9967-1.94532.1364-0.16352.5309-0.04760.249-0.1497-0.04130.01970.17940.116-0.52880.02790.0173-0.0044-0.00530.1730.0080.03324.423752.880611.1307
22.73641.4371.57841.71991.3943.81420.04360.00070.0461-0.1376-0.0159-0.0996-0.29610.1178-0.02770.05990.00660.02540.02480.00990.019441.105367.835511.9461
34.57412.21840.17272.62470.18511.7813-0.00480.1318-0.2132-0.04860.0527-0.02690.0945-0.1766-0.04790.07790.01470.01410.074-0.00070.022933.066156.33260.2743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A109 - 176
2X-RAY DIFFRACTION2B109 - 176
3X-RAY DIFFRACTION3C38 - 52

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