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- PDB-6lo2: Crystal structure of EED in complex with EZH2 peptide and compound 11# -

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Basic information

Entry
Database: PDB / ID: 6lo2
TitleCrystal structure of EED in complex with EZH2 peptide and compound 11#
Components
  • Histone-lysine N-methyltransferase EZH2
  • Polycomb protein EED
KeywordsPEPTIDE BINDING PROTEIN / HTS HIT OPTIMIZATION
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 / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development ...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 / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development / response to tetrachloromethane / primary miRNA binding / regulatory ncRNA-mediated heterochromatin formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / histone H3K27 methyltransferase activity / facultative heterochromatin formation / positive regulation of cell cycle G1/S phase transition / ESC/E(Z) complex / negative regulation of stem cell differentiation / pronucleus / chromatin silencing complex / protein-lysine N-methyltransferase activity / cardiac muscle hypertrophy in response to stress / G1 to G0 transition / positive regulation of dendrite development / histone H3 methyltransferase activity / synaptic transmission, GABAergic / DNA methylation-dependent constitutive heterochromatin formation / lncRNA binding / histone methyltransferase activity / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / negative regulation of transcription elongation by RNA polymerase II / positive regulation of protein serine/threonine kinase activity / subtelomeric heterochromatin formation / ribonucleoprotein complex binding / pericentric heterochromatin / positive regulation of epithelial to mesenchymal transition / RNA polymerase II core promoter sequence-specific DNA binding / nucleosome binding / keratinocyte differentiation / protein localization to chromatin / negative regulation of cytokine production involved in inflammatory response / positive regulation of GTPase activity / positive regulation of MAP kinase activity / B cell differentiation / enzyme activator activity / hippocampus development / liver regeneration / Regulation of PTEN gene transcription / PRC2 methylates histones and DNA / transcription corepressor binding / Defective pyroptosis / stem cell differentiation / promoter-specific chromatin binding / regulation of circadian rhythm / protein modification process / PKMTs methylate histone lysines / chromatin DNA binding / cellular response to hydrogen peroxide / Activation of anterior HOX genes in hindbrain development during early embryogenesis / G1/S transition of mitotic cell cycle / HCMV Early Events / transcription corepressor activity / rhythmic process / heterochromatin formation / response to estradiol / chromatin organization / chromosome / Oxidative Stress Induced Senescence / methylation / histone binding / chromosome, telomeric region / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / synapse / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
EZH2, SET 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 / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain ...EZH2, SET 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 / 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 superfamily / SET domain profile. / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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
Chem-EJU / Polycomb protein EED / Histone-lysine N-methyltransferase EZH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsZhao, K. / Zhao, M. / Luo, X. / Zhang, H. / Chen, Z.
CitationJournal: To Be Published
Title: Structure of EED in complex with EZH2 peptide and cmpd20
Authors: Zhao, K. / Zhao, M. / Luo, X. / Zhang, H.
History
DepositionJan 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polycomb protein EED
B: Polycomb protein EED
C: Histone-lysine N-methyltransferase EZH2
D: Histone-lysine N-methyltransferase EZH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7326
Polymers91,9574
Non-polymers7752
Water5,855325
1
A: Polycomb protein EED
C: Histone-lysine N-methyltransferase EZH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3663
Polymers45,9782
Non-polymers3871
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-14 kcal/mol
Surface area16180 Å2
MethodPISA
2
B: Polycomb protein EED
D: Histone-lysine N-methyltransferase EZH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3663
Polymers45,9782
Non-polymers3871
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-15 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.310, 178.180, 50.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Polycomb protein EED / hEED / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


Mass: 42356.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EED / Production host: Escherichia coli (E. coli) / References: UniProt: O75530
#2: Protein/peptide Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


Mass: 3622.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15910
#3: Chemical ChemComp-EJU / 8-[4-[(dimethylamino)methyl]phenyl]-N-[(2-methoxyphenyl)methyl]-[1,2,4]triazolo[4,3-a]pyridin-5-amine


Mass: 387.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H25N5O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.28 Å3/Da / Density % sol: 46.07 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS pH 8.0, 15.6% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.21→178.18 Å / Num. obs: 43322 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 31.43 Å2 / Rmerge(I) obs: 0.166 / Net I/σ(I): 9.1
Reflection shellResolution: 2.21→2.21 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 400 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
PDB_EXTRACT3.25data extraction
XDSdata processing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QXV

2qxv


Resolution: 2.21→89.09 Å / Cor.coef. Fo:Fc: 0.9299 / Cor.coef. Fo:Fc free: 0.8904 / SU R Cruickshank DPI: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.269 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.202
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 2164 5.03 %RANDOM
Rwork0.18 ---
obs0.1826 43053 99.93 %-
Displacement parametersBiso max: 120.15 Å2 / Biso mean: 29.69 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--8.0729 Å20 Å20 Å2
2--2.4059 Å20 Å2
3---5.667 Å2
Refine analyzeLuzzati coordinate error obs: 0.237 Å
Refinement stepCycle: final / Resolution: 2.21→89.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 58 325 6729
Biso mean--24.39 35.16 -
Num. residues----779
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2308SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes169HARMONIC2
X-RAY DIFFRACTIONt_gen_planes939HARMONIC5
X-RAY DIFFRACTIONt_it6564HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion830SEMIHARMONIC5
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_contact7537SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6564HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8876HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion19.23
LS refinement shellResolution: 2.21→2.27 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2394 146 4.71 %
Rwork0.1929 2955 -
all0.1951 3101 -
obs--99.93 %

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