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- PDB-5vk3: Apo ctPRC2 with E840A and K852D mutations in Ezh2 -

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Basic information

Entry
Database: PDB / ID: 5vk3
TitleApo ctPRC2 with E840A and K852D mutations in Ezh2
Components
  • Histone-lysine N-methyltransferase EZH2,Polycomb protein SUZ12
  • Polycomb Protein EED
KeywordsTRANSFERASE
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
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: 2.114 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
DepositionApr 20, 2017Deposition 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)173,34210
Polymers172,8192
Non-polymers5238
Water16,214900
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-46 kcal/mol
Surface area54560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.594, 138.004, 224.366
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-920-

HOH

21B-8633-

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: 106797.461 Da / Num. of mol.: 1 / Mutation: E840A, K852D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / 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 / Water


Mass: 18.015 Da / Num. of mol.: 900 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
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: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.11→112.18 Å / Num. obs: 98691 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.88 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.067 / Net I/σ(I): 23.13
Reflection shellResolution: 2.11→2.16 Å / Redundancy: 13.4 % / Rmerge(I) obs: 3.86 / Mean I/σ(I) obs: 1.59 / CC1/2: 0.465 / Rpim(I) all: 1.09 / % possible all: 100

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Processing

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

5bjs


Resolution: 2.114→44.753 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4899 4.96 %RANDOM
Rwork0.168 ---
obs0.1704 98691 94.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.114→44.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10069 0 8 900 10977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810370
X-RAY DIFFRACTIONf_angle_d0.84514009
X-RAY DIFFRACTIONf_dihedral_angle_d8.5357089
X-RAY DIFFRACTIONf_chiral_restr0.0541491
X-RAY DIFFRACTIONf_plane_restr0.0061838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1141-2.13810.3032860.23791863X-RAY DIFFRACTION57
2.1381-2.16330.29451000.2342083X-RAY DIFFRACTION63
2.1633-2.18960.30511310.22372249X-RAY DIFFRACTION70
2.1896-2.21740.31861090.21422598X-RAY DIFFRACTION78
2.2174-2.24650.27181350.20492907X-RAY DIFFRACTION90
2.2465-2.27730.261350.20513078X-RAY DIFFRACTION93
2.2773-2.30980.25141720.21073136X-RAY DIFFRACTION95
2.3098-2.34430.2561430.19873249X-RAY DIFFRACTION100
2.3443-2.38090.22581670.19653291X-RAY DIFFRACTION100
2.3809-2.420.25871710.19153265X-RAY DIFFRACTION100
2.42-2.46170.2441820.18843269X-RAY DIFFRACTION100
2.4617-2.50650.24661640.18033281X-RAY DIFFRACTION100
2.5065-2.55470.2711560.18253292X-RAY DIFFRACTION100
2.5547-2.60680.25021960.17593242X-RAY DIFFRACTION100
2.6068-2.66350.23451860.1753291X-RAY DIFFRACTION100
2.6635-2.72540.22571590.17833267X-RAY DIFFRACTION100
2.7254-2.79360.23341780.17863237X-RAY DIFFRACTION100
2.7936-2.86910.24571710.17713307X-RAY DIFFRACTION100
2.8691-2.95350.24061640.17363294X-RAY DIFFRACTION100
2.9535-3.04880.22751840.18263280X-RAY DIFFRACTION100
3.0488-3.15780.21651820.17623283X-RAY DIFFRACTION100
3.1578-3.28420.19841780.1773292X-RAY DIFFRACTION100
3.2842-3.43360.22771900.1663274X-RAY DIFFRACTION100
3.4336-3.61450.21881840.15843327X-RAY DIFFRACTION100
3.6145-3.84090.18871590.15233303X-RAY DIFFRACTION100
3.8409-4.13720.17621660.13323341X-RAY DIFFRACTION100
4.1372-4.55320.16541830.12743320X-RAY DIFFRACTION100
4.5532-5.21120.16671780.13343328X-RAY DIFFRACTION100
5.2112-6.56230.2031970.15733381X-RAY DIFFRACTION100
6.5623-44.76320.17181930.16883464X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.5405 Å / Origin y: 17.8568 Å / Origin z: -35.3487 Å
111213212223313233
T0.0773 Å2-0.032 Å20.017 Å2-0.0928 Å20.0067 Å2--0.0752 Å2
L0.2063 °20.0129 °20.0192 °2-0.2411 °2-0.0167 °2--0.1276 °2
S0.0356 Å °0.0795 Å °0.0098 Å °0.0515 Å °-0.0065 Å °0.0488 Å °-0.0497 Å °0.0588 Å °0.0569 Å °
Refinement TLS groupSelection details: all

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