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- PDB-5ij7: Structure of Hs/AcPRC2 in complex with a pyridone inhibitor -

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Basic information

Entry
Database: PDB / ID: 5ij7
TitleStructure of Hs/AcPRC2 in complex with a pyridone inhibitor
Components
  • (Polycomb protein ...Polycomb-group proteins) x 2
  • Enhancer of Zeste Homolog 2 (EZH2),Histone-lysine N-methyltransferase EZH2
Keywordstransferase/transferase inhibitor / lysine methyltransferase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / sex chromatin / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway ...regulation of kidney development / hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of striated muscle cell differentiation / sex chromatin / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / random inactivation of X chromosome / primary miRNA binding / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / response to tetrachloromethane / cerebellar cortex development / histone H3K27 methyltransferase activity / positive regulation of cell cycle G1/S phase transition / facultative heterochromatin formation / chromatin silencing complex / ESC/E(Z) complex / RSC-type complex / protein-lysine N-methyltransferase activity / negative regulation of stem cell differentiation / pronucleus / cardiac muscle hypertrophy in response to stress / synaptic transmission, GABAergic / G1 to G0 transition / lncRNA binding / positive regulation of dendrite development / histone H3 methyltransferase activity / negative regulation of gene expression, epigenetic / : / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / histone methyltransferase activity / oligodendrocyte differentiation / negative regulation of transcription elongation by RNA polymerase II / Transcriptional Regulation by E2F6 / subtelomeric heterochromatin formation / negative regulation of cell differentiation / enzyme activator activity / negative regulation of cytokine production involved in inflammatory response / positive regulation of epithelial to mesenchymal transition / RNA polymerase II core promoter sequence-specific DNA binding / ribonucleoprotein complex binding / pericentric heterochromatin / heterochromatin formation / keratinocyte differentiation / protein localization to chromatin / methylated histone binding / SUMOylation of chromatin organization proteins / B cell differentiation / transcription corepressor binding / PRC2 methylates histones and DNA / Regulation of PTEN gene transcription / Defective pyroptosis / liver regeneration / promoter-specific chromatin binding / stem cell differentiation / hippocampus development / G1/S transition of mitotic cell cycle / protein modification process / positive regulation of MAP kinase activity / positive regulation of protein serine/threonine kinase activity / regulation of circadian rhythm / chromatin DNA binding / cellular response to hydrogen peroxide / PKMTs methylate histone lysines / positive regulation of GTPase activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / rhythmic process / response to estradiol / chromosome / chromatin organization / methylation / Oxidative Stress Induced Senescence / cell population proliferation / chromosome, telomeric region / nuclear body / ribonucleoprotein complex / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / synapse / chromatin binding / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol
Similarity search - Function
EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / : / Ezh2, MCSS domain / 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 ...EZH2, SET domain / Polycomb protein, VEFS-Box / VEFS-Box of polycomb protein / : / Ezh2, MCSS domain / 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 / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain / CXC domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SET domain superfamily / SET domain / SANT/Myb domain / SET domain profile. / SET domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Zinc finger C2H2 type domain signature. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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 / 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 / SAD / Resolution: 2.62 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 / pdbx_struct_conn_angle / software / 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 / _software.name / _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: 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)275,96222
Polymers273,9746
Non-polymers1,98916
Water64936
1
A: 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)137,98111
Polymers136,9873
Non-polymers9948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14120 Å2
ΔGint-78 kcal/mol
Surface area42060 Å2
MethodPISA
2
B: 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)137,98111
Polymers136,9873
Non-polymers9948
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14100 Å2
ΔGint-82 kcal/mol
Surface area42640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.575, 115.042, 153.033
Angle α, β, γ (deg.)90.00, 102.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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: 72941.484 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

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Polycomb protein ... , 2 types, 4 molecules EFST

#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 / Polycomb-group proteins / 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
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

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Non-polymers , 3 types, 52 molecules

#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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 24.0 %w/v PEG monomethyl ether 2000, 0.0050 M TCEP hydrochloride, 0.1 M Bis_tris (pH 6.60)

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.62→149.39 Å / Num. obs: 70687 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 73.7 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.6
Reflection shellResolution: 2.62→3.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 4.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
autoPROCdata scaling
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.62→91.15 Å / Cor.coef. Fo:Fc: 0.9277 / Cor.coef. Fo:Fc free: 0.8969 / SU R Cruickshank DPI: 0.701 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.581 / SU Rfree Blow DPI: 0.282 / SU Rfree Cruickshank DPI: 0.293
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3591 5.09 %RANDOM
Rwork0.1912 ---
obs0.1935 70532 99.6 %-
Displacement parametersBiso mean: 68.45 Å2
Baniso -1Baniso -2Baniso -3
1--14.6704 Å20 Å2-0.3362 Å2
2--18.3044 Å20 Å2
3----3.634 Å2
Refine analyzeLuzzati coordinate error obs: 0.331 Å
Refinement stepCycle: 1 / Resolution: 2.62→91.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15526 0 86 36 15648
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115954HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1421519HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5716SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes448HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2312HARMONIC5
X-RAY DIFFRACTIONt_it15954HARMONIC20
X-RAY DIFFRACTIONt_nbd15SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2018SEMIHARMONIC5
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_contact17737SEMIHARMONIC4
LS refinement shellResolution: 2.62→2.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2868 265 5.06 %
Rwork0.2318 4977 -
all0.2347 5242 -
obs--99.6 %

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