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- PDB-3rjw: Crystal structure of histone lysine methyltransferase g9a with an... -

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Basic information

Entry
Database: PDB / ID: 3rjw
TitleCrystal structure of histone lysine methyltransferase g9a with an inhibitor
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CHEMICAL PROBE / METHYLTRANSFERASE INHIBITOR / STRUCTURAL GENOMICS CONSORTIUM / SGC / 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-CIQ / S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.56 Å
AuthorsDong, A. / Wasney, G.A. / Tempel, W. / Liu, F. / Barsyte, D. / Allali-Hassani, A. / Chen, X. / Chau, I. / Hajian, T. / Senisterra, G. ...Dong, A. / Wasney, G.A. / Tempel, W. / Liu, F. / Barsyte, D. / Allali-Hassani, A. / Chen, X. / Chau, I. / Hajian, T. / Senisterra, G. / Chavda, N. / Arora, K. / Siarheyeva, A. / Kireev, D.B. / Herold, J.M. / Bochkarev, A. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Frye, S.V. / Arrowsmith, C.H. / Brown, P.J. / Jin, J. / Vedadi, M. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells.
Authors: Vedadi, M. / Barsyte-Lovejoy, D. / Liu, F. / Rival-Gervier, S. / Allali-Hassani, A. / Labrie, V. / Wigle, T.J. / Dimaggio, P.A. / Wasney, G.A. / Siarheyeva, A. / Dong, A. / Tempel, W. / ...Authors: Vedadi, M. / Barsyte-Lovejoy, D. / Liu, F. / Rival-Gervier, S. / Allali-Hassani, A. / Labrie, V. / Wigle, T.J. / Dimaggio, P.A. / Wasney, G.A. / Siarheyeva, A. / Dong, A. / Tempel, W. / Wang, S.C. / Chen, X. / Chau, I. / Mangano, T.J. / Huang, X.P. / Simpson, C.D. / Pattenden, S.G. / Norris, J.L. / Kireev, D.B. / Tripathy, A. / Edwards, A. / Roth, B.L. / Janzen, W.P. / Garcia, B.A. / Petronis, A. / Ellis, J. / Brown, P.J. / Frye, S.V. / Arrowsmith, C.H. / Jin, J.
History
DepositionApr 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
SupersessionJul 20, 2011ID: 3NNI
Revision 1.2Jul 20, 2011Group: Other
Revision 1.3Aug 3, 2011Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 13, 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_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 EHMT2
B: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,52143
Polymers65,2102
Non-polymers2,31241
Water84747
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.580, 78.083, 70.252
Angle α, β, γ (deg.)90.000, 92.160, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Fragment: Sequence database residues 913-1193
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-V2R-PRARE2
References: UniProt: Q96KQ7, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 88 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-CIQ / 2-cyclohexyl-6-methoxy-N-[1-(1-methylethyl)piperidin-4-yl]-7-(3-pyrrolidin-1-ylpropoxy)quinazolin-4-amine


Mass: 509.726 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H47N5O2
#5: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 29 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.4 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M SODIUM FORMATE, 10% ETHYLENE GLYCOL, 25% PEG-3350, 0.1M BIS-TRIS PROPANE, pH 6.5, vapor diffusion, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 20157 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.05 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.56-2.63.70.6579880.8331100
2.6-2.653.70.6710010.8571100
2.65-2.73.70.58710480.9051100
2.7-2.763.70.5319660.8911100
2.76-2.823.70.49110080.9411100
2.82-2.883.70.37210010.917199.9
2.88-2.963.70.35410070.9291100
2.96-3.043.70.32210020.973199.8
3.04-3.123.70.24110101.016199.9
3.12-3.233.70.1889970.993199.8
3.23-3.343.70.15110091.055199.8
3.34-3.473.70.1279941.079199.8
3.47-3.633.80.11210071.107199.9
3.63-3.823.70.08410101.206199.7
3.82-4.063.70.07310301.1321100
4.06-4.383.70.06410041.283199.9
4.38-4.823.70.05510091.325199.9
4.82-5.513.70.0510181.1491100
5.51-6.943.70.04710231.1091100
6.94-503.40.03410251.303197.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K5K

3k5k


Resolution: 2.56→43.25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.627 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.568 / SU Rfree Blow DPI: 0.282 / SU Rfree Cruickshank DPI: 0.29
Details: Restraints for the refinement of the ligand CIQ were prepared using the prodrg server. WEAK ELECTRON DENSITY FOR THE QUINAZOLINE SUBSTITUENTS prevents UNAMBIGUOUS ASSIGNMENT OF THEIR ...Details: Restraints for the refinement of the ligand CIQ were prepared using the prodrg server. WEAK ELECTRON DENSITY FOR THE QUINAZOLINE SUBSTITUENTS prevents UNAMBIGUOUS ASSIGNMENT OF THEIR ROTAMERIC STATES. Model geometry was validated periodically on the molprobity server. Coot was used for interactive model re-building. Non-crystallographic symmetry restraints where applied with the autobuster -autoncs switch. Coinciding with random selection of "free" reflections for cross-validation, these restraints may have introduced additional bias and disproportionately reduced the "free" residual.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1008 5.1 %RANDOM
Rwork0.195 ---
obs0.198 19771 --
Displacement parametersBiso mean: 62.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.428 Å20 Å22.29 Å2
2---4.632 Å20 Å2
3---13.06 Å2
Refine analyzeLuzzati coordinate error obs: 0.388 Å
Refinement stepCycle: LAST / Resolution: 2.56→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 163 47 4301
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094319HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.015874HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1403SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes112HARMONIC2
X-RAY DIFFRACTIONt_gen_planes635HARMONIC5
X-RAY DIFFRACTIONt_it4237HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion16.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion559SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance32HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4753SEMIHARMONIC4
LS refinement shellResolution: 2.56→2.7 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.256 141 4.88 %
Rwork0.225 2748 -
all0.227 2889 -
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)
15.11090.8121-0.9271.7148-0.35591.74970.1679-1.0690.40020.3881-0.06980.4588-0.05880.3117-0.0981-0.21380.03530.0924-0.1306-0.05930.1146-1.3520.34743.934
25.17060.1785-1.29211.3017-0.03591.43460.02530.64360.1955-0.17980.06810.011-0.1453-0.0125-0.0934-0.2189-0.01720.0023-0.152-0.02580.079613.41460.10211.2678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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