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- PDB-6d08: Crystal structure of an engineered bump-hole complex of mutant hu... -

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Basic information

Entry
Database: PDB / ID: 6d08
TitleCrystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1 (CBX1) with H3K9bn peptide
Components
  • Chromobox protein homolog 1
  • Histone H3.1
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 / pericentric heterochromatin / Chromatin modifying enzymes / : ...chromocenter / histone methyltransferase binding / male pronucleus / female pronucleus / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / Chromatin modifying enzymes / : / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / spindle / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / chromosome, telomeric region / nuclear body / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / DNA damage response / chromatin binding / chromatin / enzyme binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane
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 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. / 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 / 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
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chromobox protein homolog 1
C: Histone H3.1
B: Chromobox protein homolog 1
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,64710
Polymers16,0864
Non-polymers5616
Water68538
1
A: Chromobox protein homolog 1
C: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3235
Polymers8,0432
Non-polymers2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-5 kcal/mol
Surface area4470 Å2
MethodPISA
2
B: Chromobox protein homolog 1
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3235
Polymers8,0432
Non-polymers2803
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-19 kcal/mol
Surface area4410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.191, 34.052, 35.267
Angle α, β, γ (deg.)76.79, 89.89, 65.10
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: 6390.145 Da / Num. of mol.: 2 / Fragment: UNP residues 20-73 / Mutation: Y3F, F27G
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/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: 1652.920 Da / Num. of mol.: 2 / Fragment: H3K9bn 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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citrate, pH 5.0, 3 M ammonium sulfate

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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 RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25.95 Å / Num. obs: 7149 / % possible obs: 90.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 3.8 / % possible all: 87.4

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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 6D07

6d07


Resolution: 2.1→23.283 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 33.6
RfactorNum. reflection% reflection
Rfree0.2524 718 10.07 %
Rwork0.2267 --
obs0.2293 7130 90.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→23.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 34 38 1072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021044
X-RAY DIFFRACTIONf_angle_d0.4451394
X-RAY DIFFRACTIONf_dihedral_angle_d17.643621
X-RAY DIFFRACTIONf_chiral_restr0.041144
X-RAY DIFFRACTIONf_plane_restr0.002176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.26220.3071450.24481235X-RAY DIFFRACTION87
2.2622-2.48960.35351280.2551225X-RAY DIFFRACTION87
2.4896-2.84930.31141370.27911275X-RAY DIFFRACTION89
2.8493-3.58770.2461540.22671324X-RAY DIFFRACTION94
3.5877-23.28490.20811540.20051353X-RAY DIFFRACTION95

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