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- PDB-5v9i: Crystal structure of catalytic domain of G9a with MS0105 -

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Basic information

Entry
Database: PDB / ID: 5v9i
TitleCrystal structure of catalytic domain of G9a with MS0105
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE / EHMT2 / BAT8 / methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
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 / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / synaptonemal complex assembly ...regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / fertilization / DNA methylation-dependent constitutive heterochromatin formation / cellular response to cocaine / organ growth / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA replication / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / behavioral response to cocaine / Transcriptional Regulation by VENTX / spermatid development / long-term memory / response to fungicide / cellular response to starvation / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / transcription corepressor binding / Transferases; Transferring one-carbon groups; Methyltransferases / 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 / p53 binding / cellular response to xenobiotic stimulus / Senescence-Associated Secretory Phenotype (SASP) / response to ethanol / nuclear speck / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 motif / Pre-SET domain / 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 motif / Pre-SET domain / 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 / SET domain superfamily / 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-90P / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å
AuthorsDong, A. / Zeng, H. / Liu, J. / Xiong, Y. / Babault, N. / Jin, J. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Dong, A. / Zeng, H. / Liu, J. / Xiong, Y. / Babault, N. / Jin, J. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Wu, H. / Brown, P.J. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of catalytic domain of G9a with MS0105
Authors: Zeng, H. / Dong, A. / Liu, J. / Xiong, Y. / Babault, N. / Jin, J. / Walker, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Wu, H. / Brown, P.J.
History
DepositionMar 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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 EHMT2
B: Histone-lysine N-methyltransferase EHMT2
C: Histone-lysine N-methyltransferase EHMT2
D: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,59941
Polymers130,4204
Non-polymers5,17937
Water12,611700
1
A: Histone-lysine N-methyltransferase EHMT2
B: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,93823
Polymers65,2102
Non-polymers2,72821
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-13 kcal/mol
Surface area24150 Å2
MethodPISA
2
C: Histone-lysine N-methyltransferase EHMT2
D: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,66118
Polymers65,2102
Non-polymers2,45216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-11 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.607, 77.509, 134.794
Angle α, β, γ (deg.)90.000, 91.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4 / Fragment: 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(DE3)
References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

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Non-polymers , 6 types, 737 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-90P / N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine


Mass: 427.583 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H37N5O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 700 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 119624 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.75 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.064 / Rrim(I) all: 0.121 / Χ2: 1.817 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.74-1.773.50.5960.8750.3740.7050.735100
1.77-1.83.60.5220.9160.3210.6140.771100
1.8-1.843.60.4670.8870.2880.550.842100
1.84-1.873.60.4180.9340.2570.4910.88100
1.87-1.923.60.3410.9530.2090.4010.929100
1.92-1.963.60.290.9670.1780.3411.013100
1.96-2.013.60.250.9670.1530.2941.088100
2.01-2.063.60.2170.9780.1330.2551.184100
2.06-2.123.60.1890.9830.1160.2221.319100
2.12-2.193.60.1760.9830.1080.2071.416100
2.19-2.273.60.1540.9870.0950.1821.58299.8
2.27-2.363.60.140.9890.0850.1641.71899.9
2.36-2.473.60.1310.9880.080.1541.76499.9
2.47-2.63.60.1170.9910.0720.1371.92699.8
2.6-2.763.60.1050.9910.0640.1232.1499.8
2.76-2.983.60.0930.9950.0580.112.49899.7
2.98-3.273.60.0880.9920.0550.1043.14899.3
3.27-3.753.50.0790.9920.050.0933.8198.7
3.75-4.723.40.0710.9930.0450.0844.14898
4.72-503.50.0660.9950.0410.0783.67198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data scaling
BUSTER2.10.2refinement
PDB_EXTRACT3.22data extraction
PHASERphasing
HKLdata scaling
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O8J

2o8j


Resolution: 1.74→25.48 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1188 1 %RANDOM
Rwork0.234 ---
obs0.234 119034 99.6 %-
Displacement parametersBiso max: 114.05 Å2 / Biso mean: 29.07 Å2 / Biso min: 10.93 Å2
Baniso -1Baniso -2Baniso -3
1-4.7996 Å20 Å24.9156 Å2
2---3.661 Å20 Å2
3----1.1386 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.74→25.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8321 0 300 704 9325
Biso mean--28.9 32.95 -
Num. residues----1064
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3200SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1480HARMONIC5
X-RAY DIFFRACTIONt_it9048HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1183SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11205SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9048HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12322HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion14.52
LS refinement shellResolution: 1.74→1.78 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 99 1.12 %
Rwork0.234 8710 -
all0.234 8809 -
obs--99.99 %
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)
11.5986-0.04550.86620.69480.16011.2462-0.098-0.47960.00430.21420.1972-0.1281-0.02-0.3202-0.09920.17660.1075-0.03410.3161-0.04270.1058-1.5361.012976.236
22.5518-0.20380.68970.4805-0.10690.5932-0.00880.13310.0808-0.06160.0520.02120.04320.031-0.04320.1063-0.0131-0.0010.0950.02190.1026-16.2631.673843.8565
31.14230.13510.44540.65320.19510.98330.0201-0.1295-0.05010.17240.065-0.09040.0248-0.1159-0.08510.10620.0458-0.00720.1023-0.00720.13470.0173-1.60038.8736
42.0659-0.03840.55970.6764-0.14010.7092-0.02780.21140.0604-0.10510.05620.04660.04760.037-0.02840.0781-0.02340.00620.09920.02020.1017-14.3106-0.54-23.007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|916 - A|1506 }A916 - 1506
2X-RAY DIFFRACTION2{ B|918 - B|1506 }B918 - 1506
3X-RAY DIFFRACTION3{ C|916 - C|1506 }C916 - 1506
4X-RAY DIFFRACTION4{ D|918 - D|1506 }D918 - 1506

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