[English] 日本語
Yorodumi
- PDB-3swc: GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3swc
TitleGLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide
Components
  • DNA (cytosine-5)-methyltransferase 3A
  • Histone-lysine N-methyltransferase EHMT1
KeywordsTRANSFERASE / epigenetics / non-histone lysine methylation / SET domain / protein lysine methyltransferase
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / epigenetic programming of gene expression / PRC2 methylates histones and DNA / positive regulation of cellular response to hypoxia / [histone H3]-lysine9 N-methyltransferase / transposable element silencing by piRNA-mediated DNA methylation / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / protein-cysteine methyltransferase activity / RMTs methylate histone arginines ...DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / epigenetic programming of gene expression / PRC2 methylates histones and DNA / positive regulation of cellular response to hypoxia / [histone H3]-lysine9 N-methyltransferase / transposable element silencing by piRNA-mediated DNA methylation / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / protein-cysteine methyltransferase activity / RMTs methylate histone arginines / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / cellular response to bisphenol A / facultative heterochromatin formation / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / genomic imprinting / XY body / C2H2 zinc finger domain binding / protein-lysine N-methyltransferase activity / response to vitamin A / response to ionizing radiation / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / hepatocyte apoptotic process / lncRNA binding / Transcriptional Regulation by E2F6 / cellular response to ethanol / Transcriptional Regulation by VENTX / regulation of embryonic development / chromosome, centromeric region / catalytic complex / heterochromatin / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / transcription corepressor binding / post-embryonic development / methyltransferase activity / response to cocaine / cellular response to amino acid stimulus / euchromatin / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / response to lead ion / response to toxic substance / nuclear matrix / neuron differentiation / p53 binding / response to estradiol / heterochromatin formation / positive regulation of cold-induced thermogenesis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / methylation / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase EHMT1 / DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger ...Histone-lysine N-methyltransferase EHMT1 / DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / Beta-clip-like / SET domain / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Ankyrin repeats (many copies) / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Beta Complex / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 3A / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.332 Å
AuthorsChang, Y. / Horton, J.R. / Zhang, X. / Cheng, X.
CitationJournal: Nat Commun / Year: 2011
Title: MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a.
Authors: Chang, Y. / Sun, L. / Kokura, K. / Horton, J.R. / Fukuda, M. / Espejo, A. / Izumi, V. / Koomen, J.M. / Bedford, M.T. / Zhang, X. / Shinkai, Y. / Fang, J. / Cheng, X.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 EHMT1
P: DNA (cytosine-5)-methyltransferase 3A
B: Histone-lysine N-methyltransferase EHMT1
Q: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,52614
Polymers68,2334
Non-polymers1,29210
Water3,063170
1
A: Histone-lysine N-methyltransferase EHMT1
P: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7637
Polymers34,1172
Non-polymers6465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-7 kcal/mol
Surface area13000 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase EHMT1
Q: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7637
Polymers34,1172
Non-polymers6465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-7 kcal/mol
Surface area12800 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-27 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.09, 90.22, 95.40
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Histone-lysine N-methyltransferase EHMT1 / Euchromatic histone-lysine N-methyltransferase 1 / Eu-HMTase1 / G9a-like protein 1 / GLP / GLP1 / ...Euchromatic histone-lysine N-methyltransferase 1 / Eu-HMTase1 / G9a-like protein 1 / GLP / GLP1 / Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Lysine N-methyltransferase 1D


Mass: 32830.219 Da / Num. of mol.: 2 / Fragment: unp residues 982-1266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D / Plasmid: pXC681 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H9B1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Protein/peptide DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / DNA methyltransferase MmuIIIA / DNA MTase MmuIIIA / M.MmuIIIA


Mass: 1286.509 Da / Num. of mol.: 2 / Fragment: unp residues 39-50 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
References: UniProt: O88508, DNA (cytosine-5-)-methyltransferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.33→40.78 Å / Num. obs: 29318 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 26
Reflection shellResolution: 2.33→2.4 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 5.6 / Num. unique all: 2825 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3MO5

3mo5


Resolution: 2.332→40.78 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1967 6.87 %random
Rwork0.1869 ---
obs0.1897 28620 94.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.413 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9521 Å20 Å2-0 Å2
2--5.0336 Å20 Å2
3----5.9857 Å2
Refinement stepCycle: LAST / Resolution: 2.332→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 60 170 4520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084458
X-RAY DIFFRACTIONf_angle_d1.1376040
X-RAY DIFFRACTIONf_dihedral_angle_d17.5531650
X-RAY DIFFRACTIONf_chiral_restr0.075627
X-RAY DIFFRACTIONf_plane_restr0.005802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3317-2.4150.3091600.21692184218480
2.415-2.51170.27821860.21052529252991
2.5117-2.6260.23461810.19442544254492
2.626-2.76440.22722020.20232593259394
2.7644-2.93750.27432000.20622688268897
2.9375-3.16430.27112010.20552747274799
3.1643-3.48260.2312130.196327932793100
3.4826-3.98610.21681990.16672812281299
3.9861-5.02060.18432100.150328382838100
5.0206-40.78720.18292150.1742925292598

+
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