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- PDB-5wuk: Crystal structure of EED [G255D] in complex with EZH2 peptide and... -

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Basic information

Entry
Database: PDB / ID: 5wuk
TitleCrystal structure of EED [G255D] in complex with EZH2 peptide and EED226 compound
Components
  • Histone-lysine N-methyltransferase EZH2
  • Polycomb protein EED
KeywordsGENE REGULATION / EED
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 / 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 / protein-lysine N-methyltransferase activity / cardiac muscle hypertrophy in response to stress / 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 / negative regulation of gene expression, epigenetic / lncRNA binding / 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 / 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 / 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 / regulation of circadian rhythm / chromatin DNA binding / protein modification process / 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 / 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 profile. / SET domain superfamily / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / 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-73K / Polycomb protein EED / Histone-lysine N-methyltransferase EZH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsChen, Z.
CitationJournal: Anal. Biochem. / Year: 2017
Title: Split luciferase-based biosensors for characterizing EED binders
Authors: Li, L. / Feng, L. / Shi, M. / Zeng, J. / Chen, Z. / Zhong, L. / Huang, L. / Guo, W. / Huang, Y. / Qi, W. / Lu, C. / Li, E. / Zhao, K. / Gu, J.
History
DepositionDec 19, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3544
Polymers45,8922
Non-polymers4612
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-16 kcal/mol
Surface area16510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.100, 80.280, 108.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42357.234 Da / Num. of mol.: 1 / Fragment: UNP residues 76-441 / Mutation: G255D
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: 3535.086 Da / Num. of mol.: 1 / Fragment: UNP residues 41-68 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q15910, histone-lysine N-methyltransferase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-73K / N-(furan-2-ylmethyl)-8-(4-methylsulfonylphenyl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine


Mass: 369.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N5O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% polyethylene glycol (PEG) 6000, 0.1M Bicine(pH9.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97845 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97845 Å / Relative weight: 1
ReflectionResolution: 2.03→64.52 Å / Num. obs: 30739 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 26.15 Å2 / Net I/σ(I): 5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→26 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.152 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.167 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.132
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1546 5.05 %RANDOM
Rwork0.16 ---
obs0.162 30632 99.8 %-
Displacement parametersBiso max: 98.43 Å2 / Biso mean: 27.7 Å2 / Biso min: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.5677 Å20 Å20 Å2
2--2.29 Å20 Å2
3---0.2776 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 2.03→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 32 340 3592
Biso mean--20.12 37.53 -
Num. residues----394
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1177SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes476HARMONIC5
X-RAY DIFFRACTIONt_it3332HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion421SEMIHARMONIC5
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_contact4025SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3332HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4506HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion16.97
LS refinement shellResolution: 2.03→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.214 152 5.11 %
Rwork0.167 2824 -
all0.17 2976 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.69530.1002-0.03140.8191-0.00851.32860.04240.02180.0610.0186-0.07350.0360.0101-0.12590.031-0.08450.02870.0103-0.0638-0.0004-0.081616.4972-7.0845-15.8961
21.5053-0.4449-0.64662.24310.80921.35690.14370.00070.29240.0627-0.15580.2571-0.2541-0.2060.0122-0.07350.07010.0269-0.0631-0.03240.04219.75557.1939-8.9694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A76 - 441
2X-RAY DIFFRACTION2{ B|* }B1

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