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- PDB-2qxv: Structural basis of EZH2 recognition by EED -

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Basic information

Entry
Database: PDB / ID: 2qxv
TitleStructural basis of EZH2 recognition by EED
Components
  • Embryonic ectoderm development
  • Enhancer of zeste homolog 2
KeywordsGENE REGULATION / WD-repeat domain / Polycomb Repressive Complex 2 / Alternative splicing / DNA-binding / Nucleus / Phosphorylation / Transcription / Transcription regulation
Function / homology
Function and homology information


negative regulation of epidermal cell differentiation / sphingomyelin phosphodiesterase activator activity / Transcriptional Regulation by E2F6 / regulation of adaxial/abaxial pattern formation / positive regulation of amide metabolic process / hepatocyte homeostasis / cellular response to trichostatin A / positive regulation of lipid metabolic process / PRC2 methylates histones and DNA / regulation of membrane lipid metabolic process ...negative regulation of epidermal cell differentiation / sphingomyelin phosphodiesterase activator activity / Transcriptional Regulation by E2F6 / regulation of adaxial/abaxial pattern formation / positive regulation of amide metabolic process / hepatocyte homeostasis / cellular response to trichostatin A / positive regulation of lipid metabolic process / PRC2 methylates histones and DNA / regulation of membrane lipid metabolic process / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / PKMTs methylate histone lysines / sex chromatin / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / epidermal cell differentiation / 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 / genomic imprinting / facultative heterochromatin formation / positive regulation of cell cycle G1/S phase transition / Oxidative Stress Induced Senescence / 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 / synaptic transmission, GABAergic / immunoglobulin heavy chain V-D-J recombination / DNA methylation-dependent constitutive heterochromatin formation / lncRNA binding / histone methyltransferase activity / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of gene expression, epigenetic / oligodendrocyte differentiation / hemopoiesis / negative regulation of transcription elongation by RNA polymerase II / regulation of neurogenesis / 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 / tumor necrosis factor-mediated signaling pathway / 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 / cellular response to leukemia inhibitory factor / enzyme activator activity / hippocampus development / liver regeneration / transcription corepressor binding / stem cell differentiation / promoter-specific chromatin binding / regulation of circadian rhythm / protein modification process / chromatin DNA binding / cellular response to hydrogen peroxide / G1/S transition of mitotic cell cycle / transcription corepressor activity / rhythmic process / response to estradiol / regulation of cell population proliferation / regulation of gene expression / methylation / sequence-specific DNA binding / 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 transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / plasma membrane
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 / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase EZH2 / Polycomb protein EED
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.82 Å
AuthorsHan, Z.
CitationJournal: Structure / Year: 2007
Title: Structural basis of EZH2 recognition by EED
Authors: Han, Z. / Xing, X. / Hu, M. / Zhang, Y. / Liu, P. / Chai, J.
History
DepositionAug 13, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Embryonic ectoderm development
B: Enhancer of zeste homolog 2


Theoretical massNumber of molelcules
Total (without water)45,3992
Polymers45,3992
Non-polymers00
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-16 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.110, 52.740, 127.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Embryonic ectoderm development / EED


Mass: 41645.340 Da / Num. of mol.: 1 / Fragment: residues in database 81-441
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: hEED / Plasmid: PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q921E6
#2: Protein/peptide Enhancer of zeste homolog 2 / EZH2 / ENX-1


Mass: 3753.315 Da / Num. of mol.: 1 / Fragment: residues 39-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ezh2, Enx1h / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q61188, histone-lysine N-methyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG MME 2000, 0.2M NaCl, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 3W1A11.1
SYNCHROTRONBSRF 3W1A20.9791, 0.9793, 0.964
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJan 7, 2005
MAR CCD 165 mm2CCDJan 7, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) double-crystalSINGLE WAVELENGTHMx-ray1
2Si(111) double-crystalMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.97911
30.97931
40.9641
ReflectionResolution: 1.82→99 Å / Num. all: 31135 / Num. obs: 30809 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rsym value: 0.062 / Net I/σ(I): 35.2
Reflection shellResolution: 1.82→1.89 Å / Rsym value: 0.36 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.82→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1526 -RANDOM
Rwork0.185 ---
all-31101 --
obs-30778 99 %-
Refinement stepCycle: LAST / Resolution: 1.82→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 0 390 3493
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.39
LS refinement shellResolution: 1.82→1.89 Å
RfactorNum. reflection% reflection
Rfree0.3086 129 -
Rwork0.2431 --
obs--89.01 %

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