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- PDB-5vsf: Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 17 -

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Basic information

Entry
Database: PDB / ID: 5vsf
TitleStructure of human GLP SET-domain (EHMT1) in complex with inhibitor 17
ComponentsHistone-lysine N-methyltransferase EHMT1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein-small molecule inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / DNA methylation-dependent heterochromatin formation / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / Transcriptional Regulation by E2F6 ...[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / DNA methylation-dependent heterochromatin formation / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / Transcriptional Regulation by E2F6 / regulation of embryonic development / Transcriptional Regulation by VENTX / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / transcription corepressor binding / methyltransferase activity / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / chromatin organization / positive regulation of cold-induced thermogenesis / 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 domain / Pre-SET motif / 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 domain / Pre-SET motif / 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 superfamily / SET domain / 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-9HG / 1,4-DIETHYLENE DIOXIDE / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsBabault, N. / Xiong, Y. / Liu, J. / Jin, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM103893 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122749 United States
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 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)62,85617
Polymers60,4652
Non-polymers2,39115
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-8 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.851, 96.088, 102.101
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1006 through 1178 or resid 1182 through 1266))
21chain B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASPASP(chain A and (resid 1006 through 1178 or resid 1182 through 1266))AA1006 - 11781 - 173
12GLYGLYSERSER(chain A and (resid 1006 through 1178 or resid 1182 through 1266))AA1182 - 1266177 - 261
21VALVALZNZNchain BBB - O1006 - 30051

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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: GLP catalytic SET-domain 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 , 6 types, 507 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-9HG / N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine


Mass: 399.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H33N5O2
#5: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 59.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 9
Details: 10 % PEG 20K, 1.4% v/v 1,4-Dioxane, 10% glycerol, 0 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-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: 1.7→19.96 Å / Num. all: 78227 / Num. obs: 78227 / % possible obs: 96.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.27 Å2 / Rpim(I) all: 0.031 / Rrim(I) all: 0.082 / Rsym value: 0.076 / Net I/av σ(I): 8.2 / Net I/σ(I): 15.5 / Num. measured all: 519519
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.7-1.796.60.6281.2114240.2620.6820.62897.3
1.79-1.96.80.4141.80.170.4480.41497.4
1.9-2.036.20.282.50.1210.3060.2896.8
2.03-2.196.80.1634.50.0660.1760.16395.4
2.19-2.46.60.1146.30.0470.1240.11492.6
2.4-2.696.70.0779.30.0320.0830.07791.9
2.69-3.16.60.05412.50.0230.0590.05495.7
3.1-3.870.043150.0170.0460.04399.7
3.8-5.386.60.03617.50.0150.0390.03699.5
5.38-19.9626.50.03815.60.0160.0410.03896.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3hna


Resolution: 1.7→19.962 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.72
RfactorNum. reflection% reflection
Rfree0.1853 3779 4.84 %
Rwork0.1605 --
obs0.1617 78148 95.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.51 Å2 / Biso mean: 26.5202 Å2 / Biso min: 10.25 Å2
Refinement stepCycle: final / Resolution: 1.7→19.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 138 492 4825
Biso mean--27.66 31.65 -
Num. residues----519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074434
X-RAY DIFFRACTIONf_angle_d1.0966002
X-RAY DIFFRACTIONf_chiral_restr0.063617
X-RAY DIFFRACTIONf_plane_restr0.006786
X-RAY DIFFRACTIONf_dihedral_angle_d13.5812662
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2524X-RAY DIFFRACTION8.467TORSIONAL
12B2524X-RAY DIFFRACTION8.467TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72150.25611380.22792743288197
1.7215-1.74420.2561310.20942790292197
1.7442-1.7680.19871310.18642756288797
1.768-1.79330.21131330.1872756288997
1.7933-1.820.21261370.16992768290597
1.82-1.84850.19481410.17412764290597
1.8485-1.87870.21511490.1762719286897
1.8787-1.91110.24861500.20322781293197
1.9111-1.94580.23791480.20432723287196
1.9458-1.98320.22271170.17022748286597
1.9832-2.02370.19271560.16712722287896
2.0237-2.06760.19991360.16392761289796
2.0676-2.11570.21321600.1612696285696
2.1157-2.16850.18721420.1632690283294
2.1685-2.22710.20671320.16682680281293
2.2271-2.29250.25161490.17872638278793
2.2925-2.36640.18741360.17152628276492
2.3664-2.45080.23031310.1722631276292
2.4508-2.54880.20111340.17352626276091
2.5488-2.66450.18421200.16522646276692
2.6645-2.80460.17761590.16532663282294
2.8046-2.97980.18981300.16232761289195
2.9798-3.2090.17641440.16812867301199
3.209-3.53040.16561420.156829053047100
3.5304-4.03750.15981630.145328923055100
4.0375-5.0730.12921320.118729763108100
5.073-19.96310.15581380.13733039317798
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)
12.30890.4409-0.27431.76340.84916.3247-0.146-0.38470.25360.33190.06710.0549-0.3969-0.51710.09070.26670.1608-0.02670.2763-0.02250.2074-4.5323-12.55941.3464
20.48880.2824-0.09972.8281-0.0981.65640.0219-0.0021-0.11310.0698-0.0437-0.2660.13640.06930.04210.10640.0047-0.04240.1787-0.00910.2078.3856-35.293-16.0674
31.00580.2180.92022.03220.88813.81720.1062-0.0255-0.15160.0374-0.05970.02270.0778-0.1024-0.04780.1265-0.0018-0.02040.12790.0080.18394.2939-34.7229-11.9813
42.5995-0.90250.38484.56331.07972.7283-0.1521-0.41390.07410.630.00920.0835-0.2212-0.47130.18970.23180.0625-0.0040.2717-0.00110.11980.6663-21.06478.0736
54.85752.5392-0.59953.906-1.57253.9353-0.12590.2138-0.11630.122-0.0298-0.5801-0.37190.5330.11490.1911-0.0345-0.05550.1912-0.0020.208916.4193-16.4244-8.202
60.5268-0.03960.15760.85530.13083.0234-0.0444-0.0397-0.00940.11130.0233-0.0714-0.1728-0.02080.02140.11450.0037-0.03460.13660.01120.16249.8619-23.4404-2.4283
72.86522.5566-2.06394.9214-3.5665.8753-0.0098-0.01550.07120.5081-0.2326-0.3353-0.7630.51640.25020.2874-0.0653-0.11920.24730.0180.225219.8947-17.806910.4092
87.69354.19973.42728.63444.678.5231-0.0078-0.0076-0.4919-0.22030.02850.13060.4241-0.0052-0.04290.15850.0135-0.01620.11180.02630.2106-11.7811-38.0872-28.287
91.19840.11420.36782.22940.59861.1358-0.01020.0315-0.0741-0.03680.0445-0.0920.01260.0613-0.0520.11660.0075-0.01330.12490.02810.0912-4.0491-20.4737-27.0071
101.50970.34670.14232.55030.70542.5598-0.06870.00860.09150.03420.06230.1424-0.1366-0.1688-0.00110.11940.02870.00240.15310.00540.1571-13.8864-10.724-23.5118
112.1609-0.0423-0.09982.06630.27541.30060.0210.219-0.1498-0.1987-0.01920.16620.0658-0.00360.01050.14050.009-0.03160.1483-0.00790.1235-10.766-27.1661-37.2341
125.55620.2649-0.72023.3029-0.74355.5750.02320.5726-0.0234-0.4192-0.008-0.2112-0.09380.25570.00210.15720.00240.01770.2112-0.02770.1341.1861-22.5196-40.641
131.3320.33030.27791.65560.50731.8287-0.01470.162-0.0353-0.14450.02260.13-0.029-0.0675-0.0010.09840.0058-0.01690.13750.00650.1368-12.1199-19.3389-36.1129
146.00130.2968-0.72052.6858-0.47654.24220.06231.12890.1047-0.479-0.0610.1406-0.12290.03060.02650.28030.0056-0.0520.3783-0.02710.1547-12.2748-22.1723-53.2031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1006 through 1042 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1043 through 1093 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1094 through 1127 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1128 through 1150 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1151 through 1184 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1185 through 1243 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1244 through 1266 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1006 through 1023 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 1024 through 1073 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1074 through 1127 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 1128 through 1167 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 1168 through 1194 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 1195 through 1243 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 1244 through 1266 )B0

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