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- PDB-6d07: Crystal structure of the complex between human chromobox homolog ... -

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Basic information

Entry
Database: PDB / ID: 6d07
TitleCrystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide
Components
  • Chromobox protein homolog 1
  • Histone H3.1Histone H3
KeywordsPROTEIN BINDING / Lysine modification / Chromodomain / Bump-hole / Epigenetics
Function / homology
Function and homology information


chromocenter / histone methyltransferase binding / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin / epigenetic regulation of gene expression ...chromocenter / histone methyltransferase binding / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / Chromatin modifying enzymes / pericentric heterochromatin / 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 / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / 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 / nucleosome / 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 / molecular adaptor activity / nuclear body / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / intracellular membrane-bounded organelle / 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
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 ...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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsArora, S. / Horne, W.S. / Islam, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM123234 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Engineering Methyllysine Writers and Readers for Allele-Specific Regulation of Protein-Protein Interactions.
Authors: Arora, S. / Horne, W.S. / Islam, K.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 1
B: Chromobox protein homolog 1
C: Histone H3.1
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2965
Polymers16,2044
Non-polymers921
Water1,802100
1
A: Chromobox protein homolog 1
C: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1943
Polymers8,1022
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-5 kcal/mol
Surface area4390 Å2
MethodPISA
2
B: Chromobox protein homolog 1
D: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)8,1022
Polymers8,1022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-5 kcal/mol
Surface area4060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.016, 32.124, 34.053
Angle α, β, γ (deg.)99.05, 106.20, 102.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Chromobox protein homolog 1 / HP1Hsbeta / Heterochromatin protein 1 homolog beta / HP1 beta / Heterochromatin protein p25 / M31 / ...HP1Hsbeta / Heterochromatin protein 1 homolog beta / HP1 beta / Heterochromatin protein p25 / M31 / Modifier 1 protein / p25beta


Mass: 6496.267 Da / Num. of mol.: 2 / Fragment: UNP residues 20-73
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX1, CBX / Production host: Escherichia coli (E. coli) / References: UniProt: P83916
#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: 1605.885 Da / Num. of mol.: 2 / Fragment: H3K9(me)3 peptide (UNP residues 2-16) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.97 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M sodium chloride, 0.1 M Tris, pH 8.0, 30% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→26.34 Å / Num. obs: 6737 / % possible obs: 93.5 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 2.6 / % possible all: 86.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FDT

3fdt


Resolution: 2.1→26.336 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.22 / Phase error: 30.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 655 9.73 %
Rwork0.2044 --
obs0.2094 6734 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→26.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1007 0 6 100 1113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021028
X-RAY DIFFRACTIONf_angle_d0.5151383
X-RAY DIFFRACTIONf_dihedral_angle_d13.12620
X-RAY DIFFRACTIONf_chiral_restr0.043146
X-RAY DIFFRACTIONf_plane_restr0.002175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.26220.33321370.23821158X-RAY DIFFRACTION90
2.2622-2.48970.2911230.24491213X-RAY DIFFRACTION92
2.4897-2.84960.31091450.24071219X-RAY DIFFRACTION95
2.8496-3.58880.2271300.19571231X-RAY DIFFRACTION94
3.5888-26.33770.21171200.17071258X-RAY DIFFRACTION96

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