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- PDB-5wfd: Humanized mutant of the Chaetomium thermophilum Polycomb Repressi... -

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Basic information

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


histone methyltransferase activity / methylation / 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, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain ...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, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain / CXC domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Chem-A9G / Zinc finger domain-containing protein / Uncharacterized protein / SET domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.654 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
Cancer Prevention and Research Institute of Texas (CPRIT)R1119 United States
Rita Allen Foundation United States
University of Texas Medical Center 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 / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
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)173,87311
Polymers172,8232
Non-polymers1,0509
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-43 kcal/mol
Surface area55020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.534, 136.971, 223.583
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: 106801.656 Da / Num. of mol.: 1 / Mutation: P302I, R304Y, E850K, N851Y, K852M, V853C, Y855F
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

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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: 2.6 Å3/Da / Density % sol: 52.74 % / Description: Plate
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-propylphosphocholine

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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: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.654→50 Å / Num. obs: 52188 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.882 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.066 / Net I/σ(I): 14.6
Reflection shellResolution: 2.654→2.7 Å / Redundancy: 11.1 % / Rmerge(I) obs: 3.146 / Num. unique obs: 2541 / CC1/2: 0.535 / Rpim(I) all: 0.975 / % 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: 2.654→46.146 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 2476 4.93 %
Rwork0.1806 --
obs0.1836 50218 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.654→46.146 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9896 0 47 0 9943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210232
X-RAY DIFFRACTIONf_angle_d1.10713825
X-RAY DIFFRACTIONf_dihedral_angle_d9.216994
X-RAY DIFFRACTIONf_chiral_restr0.0611466
X-RAY DIFFRACTIONf_plane_restr0.0071807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6539-2.70490.3845650.31141602X-RAY DIFFRACTION58
2.7049-2.76020.40031200.27232253X-RAY DIFFRACTION83
2.7602-2.82020.36781120.24682530X-RAY DIFFRACTION91
2.8202-2.88580.2891340.23562599X-RAY DIFFRACTION96
2.8858-2.95790.30521320.22772718X-RAY DIFFRACTION98
2.9579-3.03790.31081600.232681X-RAY DIFFRACTION99
3.0379-3.12720.30651520.22412748X-RAY DIFFRACTION100
3.1272-3.22820.30561640.2172714X-RAY DIFFRACTION100
3.2282-3.34350.25921470.20512778X-RAY DIFFRACTION100
3.3435-3.47730.27011350.1922745X-RAY DIFFRACTION100
3.4773-3.63550.23471460.17352737X-RAY DIFFRACTION100
3.6355-3.82710.23361460.16372766X-RAY DIFFRACTION100
3.8271-4.06680.22491410.15562766X-RAY DIFFRACTION100
4.0668-4.38050.18591250.14132794X-RAY DIFFRACTION100
4.3805-4.82090.19571270.13592790X-RAY DIFFRACTION100
4.8209-5.51750.19981400.14222809X-RAY DIFFRACTION100
5.5175-6.94770.20121410.17832833X-RAY DIFFRACTION100
6.9477-46.15340.1971890.17292879X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.5816 Å / Origin y: 17.9179 Å / Origin z: -35.2824 Å
111213212223313233
T0.1647 Å2-0.0463 Å2-0.0447 Å2-0.2028 Å20.0392 Å2--0.204 Å2
L0.7137 °2-0.1857 °2-0.1146 °2-0.811 °20.0781 °2--0.7547 °2
S0.0809 Å °0.1467 Å °-0.0009 Å °-0.002 Å °-0.0561 Å °-0.0057 Å °-0.1479 Å °0.0939 Å °-0.0273 Å °
Refinement TLS groupSelection details: ALL

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