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- PDB-5tqr: ctPRC2 in an autoinhibited conformation bound to S-adenosylmethionine -

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Basic information

Entry
Database: PDB / ID: 5tqr
TitlectPRC2 in an autoinhibited conformation bound to S-adenosylmethionine
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
S-ADENOSYLMETHIONINE / 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: 2.571 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 Medical Center 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 24, 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 1.5Oct 4, 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)173,81311
Polymers172,8912
Non-polymers9229
Water4,396244
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-41 kcal/mol
Surface area55640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.454, 138.008, 223.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

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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: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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 %
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 6M / Detector: PIXEL / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.57→50 Å / Num. obs: 55206 / % possible obs: 99.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 61.82 Å2 / CC1/2: 0.89 / Rmerge(I) obs: 0.162 / Net I/σ(I): 12.79
Reflection shellResolution: 2.57→2.61 Å / Redundancy: 9 % / Rmerge(I) obs: 1.396 / Mean I/σ(I) obs: 1.63 / CC1/2: 0.552 / % possible all: 99.6

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Processing

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

5bjs


Resolution: 2.571→47.322 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 2733 4.95 %RANDOM
Rwork0.1744 ---
obs0.1774 55206 95.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.571→47.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10208 0 35 244 10487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910539
X-RAY DIFFRACTIONf_angle_d0.9914241
X-RAY DIFFRACTIONf_dihedral_angle_d8.6287198
X-RAY DIFFRACTIONf_chiral_restr0.0561516
X-RAY DIFFRACTIONf_plane_restr0.0061868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5706-2.61490.31331000.26671828X-RAY DIFFRACTION67
2.6149-2.66240.35141260.25852135X-RAY DIFFRACTION78
2.6624-2.71360.33161210.23162259X-RAY DIFFRACTION84
2.7136-2.7690.27671200.21622486X-RAY DIFFRACTION91
2.769-2.82920.2811160.21832657X-RAY DIFFRACTION97
2.8292-2.8950.27621340.21462684X-RAY DIFFRACTION98
2.895-2.96740.28511640.20812658X-RAY DIFFRACTION99
2.9674-3.04760.27591320.20572728X-RAY DIFFRACTION99
3.0476-3.13730.23681360.21152692X-RAY DIFFRACTION98
3.1373-3.23860.27651410.19382728X-RAY DIFFRACTION100
3.2386-3.35430.22351340.19392746X-RAY DIFFRACTION100
3.3543-3.48850.27231420.19122743X-RAY DIFFRACTION100
3.4885-3.64720.2271560.17922711X-RAY DIFFRACTION100
3.6472-3.83950.25321520.16962716X-RAY DIFFRACTION99
3.8395-4.07990.2011350.15782732X-RAY DIFFRACTION99
4.0799-4.39470.2091430.142744X-RAY DIFFRACTION100
4.3947-4.83660.16831560.13042749X-RAY DIFFRACTION100
4.8366-5.53550.20251370.13912783X-RAY DIFFRACTION100
5.5355-6.97060.23191530.16542801X-RAY DIFFRACTION99
6.9706-47.330.19721350.1632893X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.7986 Å / Origin y: 17.7375 Å / Origin z: -35.0451 Å
111213212223313233
T0.2634 Å2-0.0369 Å2-0.0298 Å2-0.2181 Å20.0407 Å2--0.2174 Å2
L0.6069 °20.0066 °2-0.0382 °2-0.7634 °20.0377 °2--0.6301 °2
S0.0522 Å °0.0965 Å °0.0474 Å °0.0268 Å °-0.014 Å °0.0175 Å °-0.1434 Å °0.1205 Å °-0.0372 Å °
Refinement TLS groupSelection details: all

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