[English] 日本語
Yorodumi
- PDB-5vsc: Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vsc
TitleStructure of human G9a SET-domain (EHMT2) in complex with inhibitor 13
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein-small molecule inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of protein modification process / histone H3K56 methyltransferase activity / : / phenotypic switching / neuron fate specification / : / [histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity ...regulation of protein modification process / histone H3K56 methyltransferase activity / : / phenotypic switching / neuron fate specification / : / [histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / fertilization / : / cellular response to cocaine / : / organ growth / Transcriptional Regulation by E2F6 / spermatid development / behavioral response to cocaine / regulation of DNA replication / RNA Polymerase I Transcription Initiation / Transcriptional Regulation by VENTX / long-term memory / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to starvation / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / cellular response to xenobiotic stimulus / p53 binding / 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 domain / Pre-SET motif / 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 domain / Pre-SET motif / 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 superfamily / SET domain / 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-9HJ / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsBabault, N. / Xiong, Y. / Liu, J. / Jin, J.
CitationJournal: Bioorg. Med. Chem. / Year: 2017
Title: Structure-activity relationship studies of G9a-like protein (GLP) inhibitors.
Authors: Xiong, Y. / Li, F. / Babault, N. / Wu, H. / Dong, A. / Zeng, H. / Chen, X. / Arrowsmith, C.H. / Brown, P.J. / Liu, J. / Vedadi, M. / Jin, J.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,53314
Polymers63,4662
Non-polymers2,06712
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-9 kcal/mol
Surface area25660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.440, 78.430, 73.060
Angle α, β, γ (deg.)90.000, 90.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 918 through 1090 or resid 1095 through 1190))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA918 - 2000
211(chain B and (resid 918 through 1090 or resid 1095 through 1190))B918 - 1090
221(chain B and (resid 918 through 1090 or resid 1095 through 1190))B1095 - 1190

-
Components

#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: 31732.984 Da / Num. of mol.: 2 / Fragment: G9a catalytic SET-domain residues 916-1190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL
References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-9HJ / 6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)-N~2~-propylquinazoline-2,4-diamine


Mass: 373.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H31N5O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7.5 / Details: 20 % PEG3350, 10% glycerol, 0.2 M Sodium bromide

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→73.05 Å / Num. all: 119728 / Num. obs: 119728 / % possible obs: 95.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 17.95 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Rsym value: 0.062 / Net I/av σ(I): 5.3 / Net I/σ(I): 12.4 / Num. measured all: 779510
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.4-1.485.80.4081.80.1820.4480.40884.7
1.48-1.576.80.252.90.1020.2710.2596.8
1.57-1.676.70.1654.20.0680.1790.16597.9
1.67-1.816.10.1215.10.0530.1330.12197
1.81-1.986.90.11550.0460.1240.11598.5
1.98-2.216.70.0876.60.0360.0940.08798.6
2.21-2.566.10.0718.20.030.0770.07196.8
2.56-3.137.10.05910.10.0240.0630.05999.4
3.13-4.436.70.04911.50.020.0530.04999.3
4.43-39.0486.60.04811.60.020.0520.04894.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K5K

3k5k


Resolution: 1.4→39.048 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.61
RfactorNum. reflection% reflection
Rfree0.1817 5954 4.98 %
Rwork0.1649 --
obs0.1658 119498 95.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.87 Å2 / Biso mean: 28.8677 Å2 / Biso min: 6.69 Å2
Refinement stepCycle: final / Resolution: 1.4→39.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 116 415 4888
Biso mean--24.8 32.02 -
Num. residues----541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064563
X-RAY DIFFRACTIONf_angle_d1.0566172
X-RAY DIFFRACTIONf_chiral_restr0.091655
X-RAY DIFFRACTIONf_plane_restr0.005800
X-RAY DIFFRACTIONf_dihedral_angle_d16.081712
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2616X-RAY DIFFRACTION6.733TORSIONAL
12B2616X-RAY DIFFRACTION6.733TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.28121460.26442809295571
1.4159-1.43260.26771420.24033110325278
1.4326-1.450.25281820.22433515369789
1.45-1.46840.22771950.21153673386894
1.4684-1.48770.2111840.19953768395295
1.4877-1.50810.22341920.19613778397096
1.5081-1.52960.21661960.18363850404697
1.5296-1.55250.20031990.17383809400897
1.5525-1.57670.19421910.16983867405898
1.5767-1.60260.17872330.17153809404298
1.6026-1.63020.20072040.16943851405598
1.6302-1.65990.18292210.16953880410198
1.6599-1.69180.16522060.16893841404798
1.6918-1.72630.17612160.16413829404598
1.7263-1.76390.18582280.16423853408197
1.7639-1.80490.19672070.16113664387194
1.8049-1.850.19072180.16763877409598
1.85-1.90.19991960.16823916411299
1.9-1.9560.20551940.16913913410798
1.956-2.01910.19341950.16853939413499
2.0191-2.09120.18042190.16943870408999
2.0912-2.1750.18141980.17233904410298
2.175-2.27390.19341850.17023924410999
2.2739-2.39380.20272340.17533850408499
2.3938-2.54380.20211960.17373743393993
2.5438-2.74010.18151940.17273922411699
2.7401-3.01580.19521830.169539904173100
3.0158-3.4520.2091910.16639974188100
3.452-4.34820.14231790.14354003418299
4.3482-39.06310.1422300.14413790402094
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)
14.4076-0.993-2.70042.85031.48017.29450.12460.68450.1397-0.4315-0.07760.07320.0417-0.2449-0.03810.20410.001-0.04630.23520.02740.155114.71753.3613-12.906
21.3902-0.3802-0.46820.81870.21650.93620.04450.0953-0.0391-0.0509-0.0222-0.0035-0.014-0.06280.00760.1697-0.0233-0.01450.1112-0.00770.139128.164-1.7654-6.8746
30.7172-0.042-1.79636.1771.88724.81520.14940.14120.339-0.22790.0575-0.2422-0.6163-0.0303-0.1930.2851-0.01530.05460.13850.03080.210635.041114.3639-8.2619
41.7589-0.6341-0.48240.99810.26390.77290.03780.11920.1713-0.08120.0237-0.0567-0.1143-0.0566-0.06560.1775-0.0239-0.00020.10030.01670.143728.4385.9228-8.1206
53.3819-0.5349-0.03342.161-1.21961.24210.0770.3953-0.2339-0.5314-0.0244-0.01050.145-0.0675-0.02480.2498-0.01110.00810.1878-0.02980.140831.9511-4.9513-17.9816
63.43640.5069-1.7942.4407-1.30195.63770.19330.74740.3044-0.57860.0796-0.162-0.2035-0.106-0.21850.3366-0.00050.10330.33980.05860.268842.84798.3722-25.8837
73.33272.2335-4.15053.7061-1.53086.2517-0.21630.3024-0.4845-0.20310.14330.43110.4581-0.75920.13810.2224-0.0389-0.0270.26270.0080.34063.6622-8.780912.1033
88.59423.5522-4.51913.543-2.44823.5906-0.13010.3247-0.11120.02510.28830.44870.0117-0.4416-0.18820.1424-0.0004-0.00650.23840.04990.2318-1.912-2.576515.5933
92.6969-0.1384-0.63581.10050.07170.3624-0.1613-0.4814-0.1770.2480.1176-0.0904-0.0440.1650.03920.20720.0103-0.0070.24450.02950.175530.27942.956318.9847
103.09980.4569-1.51983.0363-0.754.69030.0072-0.85770.11530.63630.07760.0549-0.03990.13410.02220.25940.0291-0.00270.41360.04930.150527.14750.196227.1126
112.26440.0836-0.26290.6733-0.22180.9583-0.0059-0.175-0.27950.06430.03490.1163-0.0146-0.0021-0.01290.16650.010.0090.16320.06330.188713.5349-2.49820.6817
123.4004-0.3305-0.35945.23120.00555.00820.0355-0.16480.42480.26760.1790.1763-0.5509-0.2111-0.10520.17910.04820.04830.15830.0520.17657.639410.478521.0432
133.4831.6802-1.94641.6304-1.33241.44440.0202-0.3703-0.10730.2091-0.0377-0.0204-0.08460.08150.02450.17020.0188-0.00230.20540.04320.13817.54133.634725.0516
143.5094-1.3354-0.62754.27790.49452.7005-0.1018-0.604-0.25920.45690.15830.16670.00380.0177-0.04620.19930.02360.05720.3430.11030.18317.4026-0.042532.4087
153.9609-0.8592-2.09033.29292.11627.26830.1736-0.50150.20680.3857-0.0857-0.079-0.15760.3392-0.14290.35990.01670.10350.52020.07350.288-1.08945.851342.9845
167.6568-2.1108-4.4662.21981.39224.8806-0.1865-0.236-0.35570.06880.088-0.19980.23750.33890.12960.1959-0.0098-0.0080.11470.00550.214739.2164-10.9631-0.6417
175.8675-6.8985-4.58788.04945.25353.6024-0.177-0.38650.34640.12820.4678-0.63270.01560.453-0.35890.1833-0.0154-0.02860.1615-0.02470.217743.7676-4.0034-1.7763
187.5607-2.6529-0.96640.9820.30240.1536-0.00110.09720.2654-0.00040.025-0.0382-0.0291-0.0072-0.01670.222-0.0027-0.0020.15360.03210.203921.629414.30014.1303
194.2666-1.3845-1.66722.87372.53283.61570.06210.5226-0.3196-0.2311-0.26510.32370.1099-0.60170.19650.2011-0.0403-0.04870.279-0.01870.20256.86420.7817-9.0129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1002 through 1021 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 1022 through 1079 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 1080 through 1096 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 1097 through 1140 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 1141 through 1155 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 1156 through 1190 )B0
7X-RAY DIFFRACTION7chain 'A' and (resid 918 through 935 )A918 - 935
8X-RAY DIFFRACTION8chain 'A' and (resid 936 through 954 )A936 - 954
9X-RAY DIFFRACTION9chain 'A' and (resid 955 through 1001 )A955 - 1001
10X-RAY DIFFRACTION10chain 'A' and (resid 1002 through 1021 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 1022 through 1079 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 1080 through 1110 )A0
13X-RAY DIFFRACTION13chain 'A' and (resid 1111 through 1140 )A0
14X-RAY DIFFRACTION14chain 'A' and (resid 1141 through 1162 )A0
15X-RAY DIFFRACTION15chain 'A' and (resid 1163 through 1190 )A0
16X-RAY DIFFRACTION16chain 'B' and (resid 916 through 936 )B916 - 936
17X-RAY DIFFRACTION17chain 'B' and (resid 937 through 954 )B937 - 954
18X-RAY DIFFRACTION18chain 'B' and (resid 955 through 970 )B955 - 970
19X-RAY DIFFRACTION19chain 'B' and (resid 971 through 1001 )B971 - 1001

+
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