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- PDB-5tuz: Structure of human GLP SET-domain (EHMT1) in complex with inhibit... -

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Basic information

Entry
Database: PDB / ID: 5tuz
TitleStructure of human GLP SET-domain (EHMT1) in complex with inhibitor MS0124
ComponentsHistone-lysine N-methyltransferase EHMT1
KeywordsTransferase/Transferase Inhibitor / Methyl Transferase / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / facultative heterochromatin formation / C2H2 zinc finger domain binding / protein-lysine N-methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation ...[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / facultative heterochromatin formation / C2H2 zinc finger domain binding / protein-lysine N-methyltransferase activity / DNA methylation-dependent constitutive heterochromatin formation / Transcriptional Regulation by E2F6 / Transcriptional Regulation by VENTX / regulation of embryonic development / 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 / methyltransferase activity / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / positive regulation of cold-induced thermogenesis / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / nuclear body / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase EHMT1 / 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 EHMT1 / 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 / Ankyrin repeats (many copies) / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / 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-7L6 / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBabault, N. / Xiong, Y. / Liu, J. / Jin, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM103893 United States
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 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase EHMT1
B: Histone-lysine N-methyltransferase EHMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,68416
Polymers60,4652
Non-polymers2,21914
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-5 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.940, 95.780, 102.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 30232.373 Da / Num. of mol.: 2 / Fragment: UNP residues 1006-1266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL
References: UniProt: Q9H9B1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 354 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-7L6 / 6,7-dimethoxy-N-(1-methylpiperidin-4-yl)-2-(morpholin-4-yl)quinazolin-4-amine


Mass: 387.476 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N5O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 9
Details: 20% PEG 20,000, 2% (v/v) 1,4-Dioxane, 0.1 M Bicine (pH 9.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→74.94 Å / Num. obs: 54301 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.146 / Net I/σ(I): 10.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 7802 / CC1/2: 0.675 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HNA

3hna


Resolution: 1.95→59.021 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.19
RfactorNum. reflection% reflection
Rfree0.2006 2772 5.11 %
Rwork0.1614 --
obs0.1634 54238 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.17 Å2 / Biso mean: 25.3402 Å2 / Biso min: 7.22 Å2
Refinement stepCycle: final / Resolution: 1.95→59.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4174 0 126 340 4640
Biso mean--27.53 26.29 -
Num. residues----516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084432
X-RAY DIFFRACTIONf_angle_d1.0855956
X-RAY DIFFRACTIONf_chiral_restr0.052613
X-RAY DIFFRACTIONf_plane_restr0.005781
X-RAY DIFFRACTIONf_dihedral_angle_d14.0841666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.98360.25921190.225525442663100
1.9836-2.01970.28291290.197725422671100
2.0197-2.05860.2371230.191625342657100
2.0586-2.10060.22421470.179725232670100
2.1006-2.14630.20061360.173225692705100
2.1463-2.19620.21381590.169124912650100
2.1962-2.25110.21071470.168825362683100
2.2511-2.3120.20451330.16925572690100
2.312-2.380.23861450.163125552700100
2.38-2.45680.22611530.172325262679100
2.4568-2.54460.21071350.165825572692100
2.5446-2.64650.18221470.159125742721100
2.6465-2.7670.21131220.169825712693100
2.767-2.91290.20381330.170625702703100
2.9129-3.09530.21841400.173325972737100
3.0953-3.33430.1991410.1825852726100
3.3343-3.66980.19781410.163226012742100
3.6698-4.20070.17121450.142526182763100
4.2007-5.29190.16311300.123826692799100
5.2919-59.04810.17271470.13282747289499
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)
12.75680.0553-1.23134.6142-3.99344.1727-0.20810.46110.0858-0.40.2104-0.21550.29320.58730.01850.2274-0.1361-0.01830.33080.00160.17087.5314-15.20890.1852
20.95040.2633-1.64160.0742-0.42322.8398-0.10810.25090.3057-0.43730.2240.1198-0.61290.3546-0.10020.4781-0.1908-0.06880.29460.05520.2371.158-9.3089-2.8871
30.29240.7968-0.10512.078-0.59441.27180.0496-0.067-0.02280.03330.00760.23470.0257-0.1314-0.05550.10.0014-0.02870.16750.00330.1938-8.7975-30.937721.2168
41.9758-0.03531.95152.06340.32945.3490.19730.0773-0.2193-0.1747-0.03640.22750.3865-0.1852-0.10660.1482-0.0073-0.05460.0947-0.00630.2234-9.432-38.69869.6554
50.7928-0.17780.47094.7823-4.07445.4272-0.02980.1829-0.0805-0.3022-0.0998-0.1244-0.06220.40.13470.1643-0.0516-0.00880.1656-0.0130.11740.1598-27.18564.2129
61.1051-0.2230.66732.775-0.33941.9041-0.1189-0.03680.0608-0.25010.02660.1498-0.2371-0.01560.0640.1302-0.0039-0.05990.1269-0.01520.1262-7.4403-20.45162.5119
75.7844-3.33620.05353.86341.81025.9120.0856-0.0578-0.0945-0.3731-0.16180.7385-0.6471-0.8324-0.06440.26620.0726-0.11420.2659-0.05360.2475-18.451-14.96836.4261
80.5223-0.0059-0.01060.9777-0.13462.5747-0.01370.0253-0.038-0.1542-0.00280.1447-0.1948-0.0680.01650.13780.0143-0.0490.119-0.01480.1571-10.9208-22.21685.6379
93.07750.64771.22012.2398-1.01731.301-0.0250.5092-0.0071-0.4030.0021-0.02480.06770.04120.05960.2257-0.0066-0.03010.1838-0.02260.1-6.7783-26.6989-7.6236
102.8521-2.9928-1.17744.69161.92113.6459-0.1186-0.08540.1402-0.434-0.19050.2795-0.9738-0.4570.26530.35470.0787-0.16320.249-0.03360.2596-20.0299-17.7096-10.2927
116.0666-3.32452.87892.6423-3.46217.0739-0.02630.0151-0.45180.22210.0021-0.03260.54350.12290.03830.22420.0048-0.01680.1377-0.00990.272211.7971-37.984728.2724
124.3416-2.32461.33952.6979-0.46291.16390.085-0.3342-0.56420.14880.0038-0.01970.3902-0.0701-0.10830.236-0.0161-0.01770.15760.04840.26998.3066-38.919536.6886
130.5423-1.31841.51594.1267-4.58175.0493-0.0227-0.09670.02030.3308-0.00440.4141-0.3134-0.0471-0.09480.15030.0038-0.00080.1627-0.02690.2296-6.7497-15.430226.6126
141.9892-0.04710.30672.4299-0.44932.1992-0.08010.07360.1427-0.13320.0519-0.1114-0.14350.16220.02550.1195-0.03610.0020.12510.00350.135313.1561-8.984721.8109
152.48862.0638-1.46175.4281-0.77311.74310.011-0.254-0.3230.2964-0.1823-0.57360.20940.32040.20980.11480.0285-0.06320.16280.04350.238718.6781-31.481537.0766
166.80090.2374-1.99542.4022-0.04473.0428-0.018-0.3726-0.01750.2911-0.02990.2981-0.0415-0.23430.0480.13220.00790.01480.15780.00660.1435-0.2915-21.085637.2626
174.30780.033-1.40355.27440.95545.24830.034-0.5754-0.18660.4433-0.00320.2707-0.0057-0.2620.01490.1303-0.03610.00850.21460.03860.13050.2723-23.894640.1497
181.8026-0.67581.20493.9082-2.98076.6406-0.0402-0.31750.03370.392-0.0298-0.3107-0.08880.21490.08790.0955-0.0171-0.02290.1607-0.00940.13814.8633-19.130640.3156
190.64410.29260.12751.7679-0.09242.0061-0.0346-0.133-0.11680.20.0165-0.1295-0.0680.07650.01380.0793-0.0113-0.01580.09330.00390.119411.4017-17.908734.0518
205.94870.7931-0.88652.12370.23753.06150.0904-1.4513-0.18540.6184-0.1678-0.1636-0.0801-0.05250.08120.34220.0092-0.06610.45050.0370.145812.2853-22.059653.1193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1006 through 1023 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1024 through 1042 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1043 through 1073 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1074 through 1109 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1110 through 1137 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1138 through 1167 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1168 through 1184 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1185 through 1228 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1229 through 1243 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 1244 through 1266 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 1006 through 1023 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1024 through 1042 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 1043 through 1058 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 1059 through 1127 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 1128 through 1150 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 1151 through 1167 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 1168 through 1198 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 1199 through 1212 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 1213 through 1243 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 1244 through 1266 )B0

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