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

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Basic information

Entry
Database: PDB / ID: 5wfc
TitleHumanized mutant of the Chaetomium thermophilum Polycomb Repressive Complex 2 bound to the inhibitor GSK343
Components
  • Histone H3.1Histone H3
  • 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 / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events ...histone methyltransferase activity / Chromatin modifying enzymes / epigenetic regulation of gene expression / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / methylation / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / 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-A97 / Zinc finger domain-containing protein / Uncharacterized protein / SET domain-containing protein / Histone H3.1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.282 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: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact / struct_conn
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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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

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Assembly

Deposited unit
A: Polycomb Protein EED
B: Histone-lysine-N-methyltransferase EZH2, Polycomb protein SUZ12 chimera
D: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,03412
Polymers173,9693
Non-polymers1,0659
Water11,458636
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-49 kcal/mol
Surface area53970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.587, 137.794, 222.332
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
11B-8469-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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


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

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Protein/peptide , 1 types, 1 molecules D

#3: Protein/peptide Histone H3.1 / Histone H3 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1146.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

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Non-polymers , 3 types, 645 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-A97 / N-[(6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl)methyl]-6-[2-(4-methylpiperazin-1-yl)pyridin-4-yl]-1-(propan-2-yl)-1H-indazole-4-carboxamide


Mass: 541.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H39N7O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 636 / 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: 2.59 Å3/Da / Density % sol: 52.48 % / 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: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.282→50 Å / Num. obs: 79303 / % possible obs: 99.1 % / Redundancy: 12 % / CC1/2: 0.925 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.033 / Net I/σ(I): 24.6
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.126 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 3729 / CC1/2: 0.476 / Rpim(I) all: 0.454 / % possible all: 91.4

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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: 2.282→44.723 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2031 4072 5.14 %
Rwork0.1665 --
obs0.1684 79297 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.282→44.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9866 0 48 636 10550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810201
X-RAY DIFFRACTIONf_angle_d0.88113777
X-RAY DIFFRACTIONf_dihedral_angle_d8.9726967
X-RAY DIFFRACTIONf_chiral_restr0.0541460
X-RAY DIFFRACTIONf_plane_restr0.0061797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2816-2.30850.2773850.20281588X-RAY DIFFRACTION59
2.3085-2.33660.2544920.21392018X-RAY DIFFRACTION75
2.3366-2.36620.2851180.20862152X-RAY DIFFRACTION82
2.3662-2.39730.26861410.19852378X-RAY DIFFRACTION89
2.3973-2.43020.25321370.19642510X-RAY DIFFRACTION95
2.4302-2.46490.24421320.18752638X-RAY DIFFRACTION99
2.4649-2.50170.23631440.19072684X-RAY DIFFRACTION100
2.5017-2.54080.23091290.17732660X-RAY DIFFRACTION100
2.5408-2.58240.24951440.18032690X-RAY DIFFRACTION100
2.5824-2.62690.2371560.17852635X-RAY DIFFRACTION100
2.6269-2.67470.20141590.17312678X-RAY DIFFRACTION100
2.6747-2.72610.21961390.17322657X-RAY DIFFRACTION100
2.7261-2.78180.23111360.17622676X-RAY DIFFRACTION100
2.7818-2.84220.23051540.17372654X-RAY DIFFRACTION100
2.8422-2.90830.23121600.17182654X-RAY DIFFRACTION100
2.9083-2.98110.2291450.17332666X-RAY DIFFRACTION100
2.9811-3.06160.23621550.1772671X-RAY DIFFRACTION100
3.0616-3.15170.22491410.17942696X-RAY DIFFRACTION100
3.1517-3.25340.21331200.17452702X-RAY DIFFRACTION100
3.2534-3.36970.22661630.16492671X-RAY DIFFRACTION100
3.3697-3.50450.19041440.15972678X-RAY DIFFRACTION100
3.5045-3.6640.19841490.15912679X-RAY DIFFRACTION100
3.664-3.8570.18791360.15972696X-RAY DIFFRACTION100
3.857-4.09850.15291540.14572722X-RAY DIFFRACTION100
4.0985-4.41470.16651520.13582686X-RAY DIFFRACTION100
4.4147-4.85850.19211570.13832714X-RAY DIFFRACTION100
4.8585-5.56040.15761490.14092734X-RAY DIFFRACTION100
5.5604-7.00120.19451400.17922777X-RAY DIFFRACTION100
7.0012-44.73160.16981410.18072861X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 22.4105 Å / Origin y: 17.4473 Å / Origin z: -34.5652 Å
111213212223313233
T0.172 Å2-0.0632 Å2-0.0282 Å2-0.186 Å20.0324 Å2--0.1739 Å2
L0.6233 °2-0.0583 °2-0.0065 °2-0.5621 °20.0091 °2--0.588 °2
S0.0574 Å °0.1043 Å °0.0203 Å °0.0342 Å °-0.0284 Å °-0.0055 Å °-0.1332 Å °0.1265 Å °-0.0372 Å °
Refinement TLS groupSelection details: ALL

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