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- PDB-5ij8: Structure of the primary oncogenic mutant Y641N Hs/AcPRC2 in comp... -

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Basic information

Entry
Database: PDB / ID: 5ij8
TitleStructure of the primary oncogenic mutant Y641N Hs/AcPRC2 in complex with a pyridone inhibitor
Components
  • Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
  • Polycomb protein EED
  • Polycomb protein SUZ12
Keywordstransferase/transferase inhibitor / lysine methyltransferase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway ...hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / response to tetrachloromethane / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development / primary miRNA binding / random inactivation of X chromosome / regulation of adaxial/abaxial pattern formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / histone H3K27 methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / sex chromatin / positive regulation of cell cycle G1/S phase transition / facultative heterochromatin formation / genomic imprinting / ESC/E(Z) complex / negative regulation of stem cell differentiation / RSC-type complex / protein-lysine N-methyltransferase activity / cardiac muscle hypertrophy in response to stress / histone H3K9me2/3 reader activity / chromatin silencing complex / pronucleus / positive regulation of dendrite development / G1 to G0 transition / histone H3 methyltransferase activity / histone methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / lncRNA binding / negative regulation of gene expression, epigenetic / synaptic transmission, GABAergic / : / Transcriptional Regulation by E2F6 / positive regulation of MAP kinase activity / oligodendrocyte differentiation / negative regulation of transcription elongation by RNA polymerase II / positive regulation of protein serine/threonine kinase activity / positive regulation of GTPase activity / negative regulation of cell differentiation / positive regulation of epithelial to mesenchymal transition / ribonucleoprotein complex binding / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / pericentric heterochromatin / nucleosome binding / keratinocyte differentiation / protein localization to chromatin / negative regulation of cytokine production involved in inflammatory response / liver regeneration / SUMOylation of chromatin organization proteins / B cell differentiation / cellular response to leukemia inhibitory factor / Regulation of PTEN gene transcription / transcription corepressor binding / PRC2 methylates histones and DNA / Defective pyroptosis / stem cell differentiation / hippocampus development / promoter-specific chromatin binding / enzyme activator activity / G1/S transition of mitotic cell cycle / protein-DNA complex / regulation of circadian rhythm / protein modification process / chromatin DNA binding / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / cellular response to hydrogen peroxide / HCMV Early Events / transcription corepressor activity / rhythmic process / response to estradiol / heterochromatin formation / chromosome / chromatin organization / histone binding / Oxidative Stress Induced Senescence / methylation / chromosome, telomeric region / cell population proliferation / nuclear body / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / synapse / chromatin binding / regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II
Similarity search - Function
Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain ...Polycomb protein SUZ12-like, Zn domain / EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / 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 profile. / SET domain superfamily / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Zinc finger C2H2 type domain signature. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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 / Mainly Beta
Similarity search - Domain/homology
Chem-6BN / Histone-lysine N-methyltransferase EZH2 / Polycomb protein EED / Polycomb protein SUZ12 / Histone-lysine N-methyltransferase EZH2
Similarity search - Component
Biological speciesAnolis carolinensis (green anole)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsGajiwala, K.S. / Brooun, A. / Deng, Y.-L. / Liu, W.
CitationJournal: Nat Commun / Year: 2016
Title: Polycomb repressive complex 2 structure with inhibitor reveals a mechanism of activation and drug resistance.
Authors: Brooun, A. / Gajiwala, K.S. / Deng, Y.L. / Liu, W. / Bolanos, B. / Bingham, P. / He, Y.A. / Diehl, W. / Grable, N. / Kung, P.P. / Sutton, S. / Maegley, K.A. / Yu, X. / Stewart, A.E.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 1.3Mar 6, 2024Group: 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 / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
B: Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
E: Polycomb protein EED
F: Polycomb protein EED
S: Polycomb protein SUZ12
T: Polycomb protein SUZ12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,86422
Polymers273,8756
Non-polymers1,98916
Water00
1
A: Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
F: Polycomb protein EED
T: Polycomb protein SUZ12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,93211
Polymers136,9383
Non-polymers9948
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14130 Å2
ΔGint-80 kcal/mol
Surface area42630 Å2
MethodPISA
2
B: Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
E: Polycomb protein EED
S: Polycomb protein SUZ12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,93211
Polymers136,9383
Non-polymers9948
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14020 Å2
ΔGint-79 kcal/mol
Surface area42750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.331, 115.133, 153.939
Angle α, β, γ (deg.)90.00, 103.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


Mass: 72892.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anolis carolinensis (green anole), (gene. exp.) Homo sapiens (human)
Gene: EZH2, EZH2, KMT6 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: G1KPH4, UniProt: Q15910, histone-lysine N-methyltransferase
#2: Protein Polycomb protein EED / hEED / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 41776.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O75530
#3: Protein Polycomb protein SUZ12 / Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor ...Chromatin precipitated E2F target 9 protein / ChET 9 protein / Joined to JAZF1 protein / Suppressor of zeste 12 protein homolog


Mass: 22268.748 Da / Num. of mol.: 2 / Mutation: Y641N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUZ12, CHET9, JJAZ1, KIAA0160 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q15022
#4: Chemical ChemComp-6BN / 5,8-dichloro-2-[(4-ethyl-6-methyl-2-oxo-1,2-dihydropyridin-3-yl)methyl]-7-({1-[(2R)-2-hydroxypropanoyl]piperidin-4-yl}oxy)-3,4-dihydroisoquinolin-1(2H)-one


Mass: 536.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H31Cl2N3O5
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 24.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M MES (pH 5.80)

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→115.13 Å / Num. obs: 49287 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 85 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13
Reflection shellResolution: 2.98→3.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
autoPROCdata scaling
Aimlessdata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→91.28 Å / Cor.coef. Fo:Fc: 0.9138 / Cor.coef. Fo:Fc free: 0.8697 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.387
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 2491 5.08 %RANDOM
Rwork0.1881 ---
obs0.1907 48989 99.69 %-
Displacement parametersBiso mean: 69.73 Å2
Baniso -1Baniso -2Baniso -3
1--21.1379 Å20 Å20.2059 Å2
2--16.5923 Å20 Å2
3---4.5456 Å2
Refine analyzeLuzzati coordinate error obs: 0.374 Å
Refinement stepCycle: 1 / Resolution: 2.99→91.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15500 0 86 0 15586
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115926HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1621479HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5711SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes450HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2308HARMONIC5
X-RAY DIFFRACTIONt_it15926HARMONIC20
X-RAY DIFFRACTIONt_nbd23SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion22.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2015SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17767SEMIHARMONIC4
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2839 185 5.14 %
Rwork0.2361 3416 -
all0.2387 3601 -
obs--99.69 %

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