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- PDB-5bjs: Apo ctPRC2 in an autoinhibited state -

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Basic information

Entry
Database: PDB / ID: 5bjs
TitleApo ctPRC2 in an autoinhibited state
Components
  • Histone-lysine N-methyltransferase EZH2, Polycomb protein SUZ12
  • Polycomb Protein EED
KeywordsTRANSFERASE
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 superfamily / SET domain profile. / 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
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: 2.189 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121662 United States
Welch FoundationI-1790 United States
Cancer Prevention and Research Institute of Texas (CPRIT)R1119 United States
Rita Allen Foundation United States
UT Southwestern Endowed Scholar Fund United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Polycomb repressive complex 2 in an autoinhibited state.
Authors: Bratkowski, M. / Yang, X. / Liu, X.
History
DepositionOct 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,41410
Polymers172,8912
Non-polymers5238
Water14,214789
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-48 kcal/mol
Surface area54200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.775, 137.897, 223.850
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 (fungus) / Gene: CTHT_0029920 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: G0S8H7
#2: Protein Histone-lysine N-methyltransferase EZH2, Polycomb protein SUZ12


Mass: 106869.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.67 Å3/Da / Density % sol: 54.02 % / 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 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 6M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 89897 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 39.6 Å2 / CC1/2: 0.81 / Rmerge(I) obs: 0.126 / Net I/σ(I): 14.91
Reflection shellResolution: 2.19→2.25 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1.33 / CC1/2: 0.42 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
HKL-3000data scaling
PHENIXphasing
HKL-3000data collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ch1

5ch1
PDB Unreleased entry


Resolution: 2.189→43.451 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2237 4384 4.88 %RANDOM
Rwork0.1732 ---
obs0.1757 89897 95.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.189→43.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10015 0 8 789 10812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910312
X-RAY DIFFRACTIONf_angle_d0.88413936
X-RAY DIFFRACTIONf_dihedral_angle_d8.3487028
X-RAY DIFFRACTIONf_chiral_restr0.0571493
X-RAY DIFFRACTIONf_plane_restr0.0061825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1886-2.21350.343570.25281283X-RAY DIFFRACTION43
2.2135-2.23950.2497960.24832196X-RAY DIFFRACTION74
2.2395-2.26690.28921340.24432524X-RAY DIFFRACTION85
2.2669-2.29560.27661360.2362648X-RAY DIFFRACTION92
2.2956-2.32580.27121410.22162823X-RAY DIFFRACTION95
2.3258-2.35760.26821320.22152804X-RAY DIFFRACTION96
2.3576-2.39130.25521640.21072899X-RAY DIFFRACTION98
2.3913-2.4270.2781460.21192872X-RAY DIFFRACTION98
2.427-2.46490.28321470.20822962X-RAY DIFFRACTION99
2.4649-2.50530.2561510.1962922X-RAY DIFFRACTION100
2.5053-2.54850.27021470.1912921X-RAY DIFFRACTION100
2.5485-2.59480.23411460.18422990X-RAY DIFFRACTION100
2.5948-2.64470.2351480.18722907X-RAY DIFFRACTION100
2.6447-2.69870.21891240.1842959X-RAY DIFFRACTION99
2.6987-2.75740.24391580.18212965X-RAY DIFFRACTION100
2.7574-2.82150.22281750.17852954X-RAY DIFFRACTION100
2.8215-2.89210.23131690.18482889X-RAY DIFFRACTION100
2.8921-2.97020.24581550.182971X-RAY DIFFRACTION100
2.9702-3.05760.2611630.18652966X-RAY DIFFRACTION100
3.0576-3.15630.2281500.18472955X-RAY DIFFRACTION100
3.1563-3.26910.26161520.18462986X-RAY DIFFRACTION100
3.2691-3.39990.2551530.16842951X-RAY DIFFRACTION100
3.3999-3.55460.21741380.16442990X-RAY DIFFRACTION100
3.5546-3.74190.20221500.15712992X-RAY DIFFRACTION100
3.7419-3.97620.2021640.152975X-RAY DIFFRACTION100
3.9762-4.28290.1981520.13752998X-RAY DIFFRACTION100
4.2829-4.71350.18051540.13123014X-RAY DIFFRACTION100
4.7135-5.39440.17771570.13983009X-RAY DIFFRACTION100
5.3944-6.79220.21251570.17583039X-RAY DIFFRACTION100
6.7922-43.45980.20081680.18693149X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.7223 Å / Origin y: 17.4832 Å / Origin z: -35.0659 Å
111213212223313233
T0.1739 Å2-0.0372 Å2-0.0168 Å2-0.2118 Å20.0329 Å2--0.2033 Å2
L0.5545 °2-0.0101 °2-0.0194 °2-0.778 °20.0957 °2--0.5996 °2
S0.044 Å °0.1018 Å °0.0259 Å °0.0166 Å °-0.0049 Å °0.023 Å °-0.1118 Å °0.0872 Å °-0.0358 Å °
Refinement TLS groupSelection details: all

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