[English] 日本語
Yorodumi
- PDB-4mi0: Human Enhancer of Zeste (Drosophila) Homolog 2(EZH2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mi0
TitleHuman Enhancer of Zeste (Drosophila) Homolog 2(EZH2)
ComponentsHistone-lysine N-methyltransferase EZH2
KeywordsTRANSFERASE / EZH2 / Gene regulation / chromatin modification / histone methyltransferase / transcription / gene silencing / Polycomb Repressive Complex 2 / Structural Genomics / Structural Genomics Consortium / SGC
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 / 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 / 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 / nucleus
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. / Beta-clip-like / SET domain / 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 / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Histone-lysine N-methyltransferase EZH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDong, A. / Zeng, H. / He, H. / Wernimont, A. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2013
Title: Structure of the catalytic domain of EZH2 reveals conformational plasticity in cofactor and substrate binding sites and explains oncogenic mutations.
Authors: Wu, H. / Zeng, H. / Dong, A. / Li, F. / He, H. / Senisterra, G. / Seitova, A. / Duan, S. / Brown, P.J. / Vedadi, M. / Arrowsmith, C.H. / Schapira, M.
History
DepositionAug 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-lysine N-methyltransferase EZH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,09911
Polymers26,7061
Non-polymers39210
Water1,15364
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.010, 57.796, 74.542
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Components

#1: Protein Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


Mass: 26706.416 Da / Num. of mol.: 1 / Fragment: UNP residues 520-746
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EZH2, KMT6 / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q15910, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Lithium Sulfate, 0.1M HEPES pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97904
SYNCHROTRONCLSI 08ID-121.28295
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDApr 18, 2013
RAYONIX MX300HE2CCDMay 28, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
21.282951
ReflectionRedundancy: 5 % / Number: 50360 / Rmerge(I) obs: 0.113 / Χ2: 2.6 / D res high: 2.24 Å / D res low: 50 Å / Num. obs: 10025 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.085096.210.0799.8964.6
4.826.0898.510.0714.9725
4.224.8299.210.0683.9825
3.834.229910.0824.135
3.563.8399.810.0933.7275
3.353.5699.810.1112.9385.1
3.183.3599.810.1142.2425.1
3.043.1899.810.1422.0955.1
2.923.0410010.1751.7635.2
2.822.9210010.211.4835.1
2.732.8210010.2821.3555.2
2.662.7310010.3191.3955.1
2.592.6610010.391.165.1
2.522.5910010.4451.1435.2
2.472.5210010.4741.1365.1
2.412.4710010.5721.0785.1
2.362.4110010.6331.0535
2.322.3610010.6610.9975
2.282.3299.210.8771.0244.8
2.242.2898.510.9824.4614.5
ReflectionResolution: 2→50 Å / Num. obs: 13445 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.8 / Num. unique all: 635 / % possible all: 94.1

-
Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000data scaling
ARP/wARP7.3.0model building
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2→32.06 Å / Cor.coef. Fo:Fc: 0.9281 / Cor.coef. Fo:Fc free: 0.9172 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 654 4.88 %RANDOM
Rwork0.1977 ---
obs0.1995 13414 98.08 %-
Displacement parametersBiso max: 89.68 Å2 / Biso mean: 36.1802 Å2 / Biso min: 14.95 Å2
Baniso -1Baniso -2Baniso -3
1--11.4804 Å20 Å20 Å2
2--6.5181 Å20 Å2
3---4.9623 Å2
Refine analyzeLuzzati coordinate error obs: 0.234 Å
Refinement stepCycle: LAST / Resolution: 2→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1584 0 10 64 1658
LS refinement shellResolution: 2→2.16 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2474 136 5.09 %
Rwork0.2023 2538 -
all0.2046 2674 -
obs--98.08 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more