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- PDB-5wf7: Chaetomium thermophilum Polycomb Repressive Complex 2 bound to GSK126 -

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Basic information

Entry
Database: PDB / ID: 5wf7
TitleChaetomium thermophilum Polycomb Repressive Complex 2 bound to GSK126
Components
  • Histone-lysine-N-methyltransferase EZH2, Polycomb protein SUZ12 chimera
  • Polycomb Protein EED
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / transferase / epigenetics / complex / inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


[histone H3]-lysine27 N-trimethyltransferase / histone H3K27 methyltransferase activity / heterochromatin formation / chromatin organization / methylation / chromatin binding / zinc ion binding / metal ion binding / nucleus
Similarity search - Function
EZH2, N-terminal domain / MCSS domain / : / : / Fungal MCSS domain / EZH2 N-terminal domain / Fungal polycomb repressive complex 2, Ezh2-like, preSET CXC domain / Polycomb protein EED insertion domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein ...EZH2, N-terminal domain / MCSS domain / : / : / Fungal MCSS domain / EZH2 N-terminal domain / Fungal polycomb repressive complex 2, Ezh2-like, preSET CXC domain / Polycomb protein EED insertion domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain profile. / SET domain superfamily / SET domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Chem-A9G / Polycomb protein SUZ12 / Polycomb protein EED / Histone-lysine N-methyltransferase EZH2
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBratkowski, M.A. / Liu, X.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM114576 United States
Welch FoundationI-1790 United States
Rita Allen Foundation United States
Cancer Prevention and Research Institute of Texas (CPRIT)R1119 United States
UT Southwestern Endowed Scholar Fund United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121662 United States
CitationJournal: Sci Rep / Year: 2018
Title: An Evolutionarily Conserved Structural Platform for PRC2 Inhibition by a Class of Ezh2 Inhibitors.
Authors: Bratkowski, M. / Yang, X. / Liu, X.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb Protein EED
B: Histone-lysine-N-methyltransferase EZH2, Polycomb protein SUZ12 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,94111
Polymers172,8912
Non-polymers1,0509
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10310 Å2
ΔGint-46 kcal/mol
Surface area52540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.875, 136.303, 223.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Polycomb Protein EED


Mass: 66021.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0029920 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0S8H7
#2: Protein Histone-lysine-N-methyltransferase EZH2, Polycomb protein SUZ12 chimera / Zinc finger domain-containing protein


Mass: 106869.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0053230, CTHT_0006210 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0SDW4, UniProt: G0RYC6
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A9G / 1-[(2S)-butan-2-yl]-N-[(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-3-methyl-6-[6-(piperazin-1-yl)pyridin-3-yl]-1H-indole-4-carboxamide


Mass: 526.672 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H38N6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM sodium malonate pH 7.0, 16% PEG 3350, 43 mM 3-cyclohexyl-1-propyphosphocholine

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.495→50 Å / Num. all: 61530 / Num. obs: 61696 / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 22.5
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 12.1 % / Rmerge(I) obs: 1.896 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 3047 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BJS

5bjs


Resolution: 2.5→44.14 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2875 4.99 %Random selection
Rwork0.191 ---
obs0.194 57672 93.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9730 0 47 288 10065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110048
X-RAY DIFFRACTIONf_angle_d1.04813566
X-RAY DIFFRACTIONf_dihedral_angle_d9.9226027
X-RAY DIFFRACTIONf_chiral_restr0.0561441
X-RAY DIFFRACTIONf_plane_restr0.0071765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4952-2.53610.2244620.23611160X-RAY DIFFRACTION42
2.5361-2.57980.2818960.24431644X-RAY DIFFRACTION60
2.5798-2.62670.30921090.25971925X-RAY DIFFRACTION69
2.6267-2.67730.33141310.24462553X-RAY DIFFRACTION94
2.6773-2.73190.31761330.24082766X-RAY DIFFRACTION99
2.7319-2.79130.27211570.23842790X-RAY DIFFRACTION100
2.7913-2.85620.29121530.23062716X-RAY DIFFRACTION100
2.8562-2.92760.35671390.23042762X-RAY DIFFRACTION100
2.9276-3.00680.29111350.22742791X-RAY DIFFRACTION100
3.0068-3.09520.26331520.2262771X-RAY DIFFRACTION100
3.0952-3.19510.25121410.21272777X-RAY DIFFRACTION100
3.1951-3.30930.26671490.19882773X-RAY DIFFRACTION100
3.3093-3.44170.28811330.1972801X-RAY DIFFRACTION100
3.4417-3.59830.2421540.18552765X-RAY DIFFRACTION100
3.5983-3.78790.25981410.17482780X-RAY DIFFRACTION100
3.7879-4.02510.2361420.16752813X-RAY DIFFRACTION100
4.0251-4.33560.21211600.15952773X-RAY DIFFRACTION100
4.3356-4.77140.20831520.14432797X-RAY DIFFRACTION100
4.7714-5.46080.19821460.1562841X-RAY DIFFRACTION100
5.4608-6.87580.20851490.18882860X-RAY DIFFRACTION100
6.8758-44.1490.22371410.19332939X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -21.9362 Å / Origin y: -16.6111 Å / Origin z: -34.8341 Å
111213212223313233
T0.2154 Å2-0.1505 Å20.0967 Å2-0.2472 Å2-0.0456 Å2--0.2189 Å2
L0.8937 °2-0.2936 °2-0.156 °2-0.5914 °20.2777 °2--1.1736 °2
S0.0473 Å °0.3195 Å °0.0045 Å °0.0477 Å °-0.1275 Å °-0.0051 Å °0.3254 Å °-0.235 Å °-0.0111 Å °
Refinement TLS groupSelection details: ALL

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