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- PDB-7x73: Structure of G9a in complex with RK-701 -

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Basic information

Entry
Database: PDB / ID: 7x73
TitleStructure of G9a in complex with RK-701
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE / histone lysine methyltransferase / inhibitor / protein-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 / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...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 / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-J26 / SINEFUNGIN / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsNiwa, H. / Shirai, F. / Sato, S. / Nishigaya, Y. / Shirouzu, M. / Umehara, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: A specific G9a inhibitor unveils BGLT3 lncRNA as a universal mediator of chemically induced fetal globin gene expression.
Authors: Takase, S. / Hiroyama, T. / Shirai, F. / Maemoto, Y. / Nakata, A. / Arata, M. / Matsuoka, S. / Sonoda, T. / Niwa, H. / Sato, S. / Umehara, T. / Shirouzu, M. / Nishigaya, Y. / Sumiya, T. / ...Authors: Takase, S. / Hiroyama, T. / Shirai, F. / Maemoto, Y. / Nakata, A. / Arata, M. / Matsuoka, S. / Sonoda, T. / Niwa, H. / Sato, S. / Umehara, T. / Shirouzu, M. / Nishigaya, Y. / Sumiya, T. / Hashimoto, N. / Namie, R. / Usui, M. / Ohishi, T. / Ohba, S.I. / Kawada, M. / Hayashi, Y. / Harada, H. / Yamaguchi, T. / Shinkai, Y. / Nakamura, Y. / Yoshida, M. / Ito, A.
History
DepositionMar 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,69718
Polymers65,2102
Non-polymers2,48716
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-5 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.215, 56.243, 66.475
Angle α, β, γ (deg.)76.052, 72.474, 67.533
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free synthesis / Gene: EHMT2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 6 types, 594 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Chemical ChemComp-J26 / N-[(2S)-1-[(4-cyanophenyl)amino]-4-cyclopropyl-1-oxidanylidene-butan-2-yl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1H-indole-2-carboxamide


Mass: 446.541 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H30N4O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M Bis-Tris propane (pH 7.4), 0.2M sodium formate, 10% ethylene glycol, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→42.9 Å / Num. obs: 86112 / % possible obs: 96.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 17.7 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.057 / Rsym value: 0.048 / Net I/σ(I): 15.1
Reflection shellResolution: 1.49→1.52 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4130 / CC1/2: 0.705 / Rpim(I) all: 0.516 / Rrim(I) all: 0.986 / Rsym value: 0.836

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874+SVNrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RJW

3rjw


Resolution: 1.49→42.9 Å / SU ML: 0.1636 / Cross valid method: FREE R-VALUE / Phase error: 22.8235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1933 4183 4.87 %
Rwork0.167 159946 -
obs0.1683 86078 94.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.72 Å2
Refinement stepCycle: LAST / Resolution: 1.49→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 148 578 5110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00644659
X-RAY DIFFRACTIONf_angle_d0.87236313
X-RAY DIFFRACTIONf_chiral_restr0.0758665
X-RAY DIFFRACTIONf_plane_restr0.0045823
X-RAY DIFFRACTIONf_dihedral_angle_d17.09131747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.510.30092740.29434864X-RAY DIFFRACTION87.68
1.51-1.520.26782130.2785040X-RAY DIFFRACTION88.79
1.52-1.540.29892760.27345117X-RAY DIFFRACTION89.5
1.54-1.560.32152570.26535122X-RAY DIFFRACTION89.83
1.56-1.580.26612480.25825066X-RAY DIFFRACTION90.9
1.58-1.610.27922940.24625298X-RAY DIFFRACTION92.25
1.61-1.630.28472330.23885172X-RAY DIFFRACTION92.36
1.63-1.650.29192790.23345414X-RAY DIFFRACTION94.51
1.65-1.680.23252750.22865175X-RAY DIFFRACTION94
1.68-1.710.25142790.2135409X-RAY DIFFRACTION94.17
1.71-1.740.23192830.20565377X-RAY DIFFRACTION94.3
1.74-1.770.26292740.20455313X-RAY DIFFRACTION94.41
1.77-1.80.2662910.20325359X-RAY DIFFRACTION94.89
1.8-1.840.21272980.19535261X-RAY DIFFRACTION94.64
1.84-1.880.23722550.1835514X-RAY DIFFRACTION94.92
1.88-1.920.19843030.17455207X-RAY DIFFRACTION94.8
1.92-1.970.2082900.16895447X-RAY DIFFRACTION95.3
1.97-2.020.20142990.16485310X-RAY DIFFRACTION94.84
2.02-2.080.17832620.16275482X-RAY DIFFRACTION95.48
2.08-2.150.18392110.16255457X-RAY DIFFRACTION95.55
2.15-2.230.21142510.16295376X-RAY DIFFRACTION95.6
2.23-2.310.21162500.16355441X-RAY DIFFRACTION95.68
2.31-2.420.20972230.16145496X-RAY DIFFRACTION95.8
2.42-2.550.17692590.17275479X-RAY DIFFRACTION96.05
2.55-2.710.18323080.16335409X-RAY DIFFRACTION95.96
2.71-2.920.20683310.16615321X-RAY DIFFRACTION95.89
2.92-3.210.16062790.16135411X-RAY DIFFRACTION96.08
3.21-3.670.16352650.14185524X-RAY DIFFRACTION96.94
3.67-4.630.14972980.12615506X-RAY DIFFRACTION97.42
4.63-42.90.17193250.14625579X-RAY DIFFRACTION99.19
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)
15.268457975611.88765208277-0.980638412376.25317398567-4.99816602559.02705759337-0.126893359874-0.278635327668-0.726262268927-0.12722701527-0.162530436306-0.4265327238150.9137608867630.4685683880760.3423417093950.289868600670.0277958878679-0.0001393208417930.2578746396330.04813920050110.295977869644-16.7989692575-34.950558503134.5425930337
22.91658141536-1.090600042890.8207117742946.66594604797-7.087588128648.950830481560.0454597748307-0.0599915624851-0.398585013911-0.327973740578-0.031826706809-0.0135783258090.776474612529-0.0159587095817-0.03654325114060.24809268106-0.0258118893838-0.007978152993380.2110066841490.0001891891501870.220622586421-25.0495667274-37.148179036234.587931189
31.519811922470.495428607943-0.577623337732.10191730766-0.848922626850.7312548765410.288585926731-0.5107011735210.2775057780890.63381656093-0.2364070416090.0565834394728-0.284805588270.0938667082315-0.08127933715820.33644171309-0.07320365376750.03911811966090.310156065511-0.06476975719070.179674969935-22.3025591763-4.9837421845736.2671859467
40.6818434323960.341441052377-0.6536710512382.98557182018-0.7317590992771.647943117520.125343175996-0.219189198724-0.1174470922030.2782038794-0.112639792361-0.194028800738-0.06020699381460.0759064800923-0.01355597980850.173405659842-0.0389222867955-0.03131144837640.2554167831490.004209962116360.114925932129-22.332070979-21.509907069338.5813084653
52.67842132319-0.2299223363121.355556602732.17648030262-1.97525105555.308017386130.0514060999574-0.265868718860.05265820452440.3471248641030.09975953320180.411782192462-0.146679563066-0.614122508907-0.0977296784070.173682338122-0.04263914179530.02017957321460.2473937593770.009643405791330.174306428357-34.738015633-22.928117236237.542070886
60.9708954923360.502472773886-0.4356319934881.79232734081-0.2205726037451.486752700980.19032268473-0.294319217824-0.02066891689790.490251321423-0.154308699897-0.00707080662304-0.03363433139830.10756924323-0.0004681464494260.24549942635-0.060735801421-0.01223433882810.25778175222-0.01172603316150.124615264142-26.2117705201-16.91276026941.8281319092
77.344597917041.160271279590.2762451797125.11683231703-1.455961743235.56697552771-0.0131174900463-0.357495851950.3373740687540.4934628748160.06260649397760.388980222937-0.312776333866-0.396465188711-0.04222474895070.438217087993-0.04998062878120.08631165006270.3020252042410.01535430533430.220863041443-41.6688868757-28.331997376454.6493344242
83.073184900041.86804169049-0.7714664702033.93931261898-1.282724896091.853325669690.165989248375-0.2461988691140.2931770905420.198939126238-0.188731240626-0.068975888216-0.1505875376610.07798517365850.010901456730.166198938086-0.008849404071090.02218313840180.136162935139-0.04092240496710.196565169798-1.872781400640.31295460086119.6100861084
92.014540362380.125190658649-0.6997957032294.00222665766-0.2250317209011.24131576668-0.02639033371490.145557861153-0.161079717513-0.350455679637-0.0758629082028-0.03538354026490.100145376461-0.05587140987780.08314110441110.1487553344790.0014335136153-0.01447409057160.148990177844-0.01822460063510.133007215739-18.5924552602-25.403386476412.1746398858
101.32512497520.936040524677-0.4300679808451.34546189821-0.2296190400811.328763686670.05183104451330.1089809894280.170500727759-0.0367060791550.02902844808970.090659369259-0.102914912314-0.0770586179314-0.04137544316040.1048455202060.02736615294040.004306229236260.0933879764874-0.0002926314295770.149282652935-7.22069331719-7.9316032381410.9273993563
113.75429889426-0.679365762571-1.208914851134.02881437101-0.8171171970793.455609366550.1439633422690.745520536870.609218454877-0.452831906470.02553206138060.444197924035-0.242726487654-0.384219009089-0.06893124940570.1915811922430.06574007468780.03672169376740.243742461730.07931433770110.322407538195-20.3383017064-3.188325884846.51957985808
122.392023633380.785344500842-0.6615533428832.31038386187-0.3746163869561.0840516683-0.006979434157780.1242134489160.0547571692986-0.1642287847450.0249462277420.04908680000190.0385655364475-0.0343885244955-0.01726876743060.1222694750610.0305801103212-0.01639423702260.120253526167-0.001828129566710.122592789985-9.30034481195-12.017924846.16791258109
133.918483351290.234123726416-0.008756452487344.48342226171-1.551354140168.521301279780.1405679741110.5411058489680.0245603477216-0.4742453537860.1194082382220.238597199592-0.166423345711-0.410702246627-0.2086842802270.3095053694640.05100993940390.02613836193830.314805500040.07469451783520.245992882636-5.768059437270.481574860906-10.7184417421
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 917 through 935 )AA917 - 9351 - 19
22chain 'A' and (resid 936 through 954 )AA936 - 95420 - 40
33chain 'A' and (resid 955 through 1021 )AA955 - 102141 - 107
44chain 'A' and (resid 1022 through 1079 )AA1022 - 1079108 - 165
55chain 'A' and (resid 1080 through 1118 )AA1080 - 1118166 - 206
66chain 'A' and (resid 1119 through 1155 )AA1119 - 1155207 - 243
77chain 'A' and (resid 1156 through 1190 )AA1156 - 1190244 - 278
88chain 'B' and (resid 916 through 954 )BH916 - 9541 - 43
99chain 'B' and (resid 955 through 1030 )BH955 - 103044 - 116
1010chain 'B' and (resid 1031 through 1079 )BH1031 - 1079117 - 165
1111chain 'B' and (resid 1080 through 1106 )BH1080 - 1106166 - 192
1212chain 'B' and (resid 1107 through 1155 )BH1107 - 1155193 - 245
1313chain 'B' and (resid 1156 through 1191 )BH1156 - 1191246 - 281

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