[English] 日本語
Yorodumi
- PDB-5ttf: Crystal structure of catalytic domain of G9a with MS012 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ttf
TitleCrystal structure of catalytic domain of G9a with MS012
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE / EHMT2 / G9a / BAT8 / methyltransferase / UNC3832 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of protein modification process / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly ...regulation of protein modification process / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / histone H3K56 methyltransferase activity / protein-lysine N-methyltransferase activity / oocyte development / C2H2 zinc finger domain binding / fertilization / cellular response to cocaine / organ growth / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / spermatid development / Transcriptional Regulation by E2F6 / behavioral response to cocaine / regulation of DNA replication / RNA Polymerase I Transcription Initiation / Transcriptional Regulation by VENTX / long-term memory / response to fungicide / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Transferases; Transferring one-carbon groups; Methyltransferases / epigenetic regulation of gene expression / cellular response to starvation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / cellular response to xenobiotic stimulus / Senescence-Associated Secretory Phenotype (SASP) / response to ethanol / nuclear speck / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Beta-clip-like / SET domain ...Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / 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 / Ankyrin repeat / Beta Complex / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-7KZ / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsDONG, A. / ZENG, H. / LIU, J. / XIONG, Y. / BABAULT, N. / JIN, J. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...DONG, A. / ZENG, H. / LIU, J. / XIONG, Y. / BABAULT, N. / JIN, J. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / WU, H. / BROWN, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of Potent and Selective Inhibitors for G9a-Like Protein (GLP) Lysine Methyltransferase.
Authors: Xiong, Y. / Li, F. / Babault, N. / Dong, A. / Zeng, H. / Wu, H. / Chen, X. / Arrowsmith, C.H. / Brown, P.J. / Liu, J. / Vedadi, M. / Jin, J.
History
DepositionNov 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
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_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone-lysine N-methyltransferase EHMT2
B: Histone-lysine N-methyltransferase EHMT2
C: Histone-lysine N-methyltransferase EHMT2
D: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,87934
Polymers130,4204
Non-polymers4,45930
Water10,557586
1
A: Histone-lysine N-methyltransferase EHMT2
C: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,43917
Polymers65,2102
Non-polymers2,23015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-8 kcal/mol
Surface area23940 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase EHMT2
D: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,43917
Polymers65,2102
Non-polymers2,23015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-15 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.846, 67.749, 77.845
Angle α, β, γ (deg.)92.090, 90.050, 91.800
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Histone-lysine N-methyltransferase EHMT2 / Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 ...Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 methyltransferase 3 / H3-K9-HMTase 3 / Lysine N-methyltransferase 1C / Protein G9a


Mass: 32604.924 Da / Num. of mol.: 4 / Fragment: UNP residues 879-1159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Plasmid: P28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

-
Non-polymers , 6 types, 616 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-7KZ / N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine / N~2~-hexyl-6,7-dimethoxy-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine


Mass: 401.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H35N5O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 119007 / % possible obs: 96.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.049 / Rrim(I) all: 0.09 / Χ2: 1.67 / Net I/av σ(I): 23.91 / Net I/σ(I): 9.4 / Num. measured all: 372722
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.72-1.752.50.550.82183.5
1.75-1.782.70.4860.818194.4
1.78-1.8230.4330.898195.6
1.82-1.853.20.4070.898196.1
1.85-1.893.20.3360.917196.2
1.89-1.943.20.2760.948196.4
1.94-1.993.20.2230.962196.5
1.99-2.043.20.1830.979196.8
2.04-2.13.20.160.98196.9
2.1-2.173.20.1380.984197.1
2.17-2.243.20.1190.987197.3
2.24-2.333.20.1090.988197.5
2.33-2.443.20.0980.989197.7
2.44-2.573.20.0890.991197.8
2.57-2.733.20.0760.993198.1
2.73-2.943.20.070.995198.2
2.94-3.243.20.0640.993198.3
3.24-3.713.10.0560.994198.5
3.71-4.6730.050.995198.3
4.67-503.10.050.996197.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K5K

3k5k


Resolution: 1.72→50.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.273 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1275 1.1 %RANDOM
Rwork0.2066 ---
obs0.207 117616 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.27 Å2 / Biso mean: 28.993 Å2 / Biso min: 8.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å2-1.4 Å20.33 Å2
2--0.18 Å2-0.35 Å2
3---2.27 Å2
Refinement stepCycle: final / Resolution: 1.72→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8325 0 226 588 9139
Biso mean--30.58 32.35 -
Num. residues----1059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198902
X-RAY DIFFRACTIONr_bond_other_d0.0020.028013
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.95412070
X-RAY DIFFRACTIONr_angle_other_deg1.043.00618326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86451087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16723.333432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.204151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2781579
X-RAY DIFFRACTIONr_chiral_restr0.0850.21288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210434
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022180
X-RAY DIFFRACTIONr_mcbond_it1.6222.8594277
X-RAY DIFFRACTIONr_mcbond_other1.6222.8594277
X-RAY DIFFRACTIONr_mcangle_it2.4984.2755336
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 85 -
Rwork0.297 7859 -
all-7944 -
obs--87.37 %

+
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