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- PDB-5v9j: Crystal structure of catalytic domain of GLP with MS0105 -

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Basic information

Entry
Database: PDB / ID: 5v9j
TitleCrystal structure of catalytic domain of GLP with MS0105
ComponentsHistone-lysine N-methyltransferase EHMT1
KeywordsTRANSFERASE / EHMT1 / methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC
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-90P / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.74 Å
AuthorsDong, A. / Zeng, H. / Liu, J. / Xiong, Y. / Babault, N. / Jin, J. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. ...Dong, A. / Zeng, H. / Liu, J. / Xiong, Y. / Babault, N. / Jin, J. / Tempel, W. / 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 GLP with MS0105
Authors: Zeng, H. / Dong, A. / Liu, J. / Xiong, Y. / Babault, N. / Jin, J. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Wu, H. / Brown, P.J. / Structural Genomics Consortium (SGC)
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 EHMT1
B: Histone-lysine N-methyltransferase EHMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,30831
Polymers65,9492
Non-polymers2,36029
Water11,367631
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-38 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.848, 95.891, 102.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsTHE AUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN.

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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: 32974.344 Da / Num. of mol.: 2 / Fragment: residues 982-1266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D / Plasmid: PET28-LIC / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21-V2R-PRARE2
References: UniProt: Q9H9B1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

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Non-polymers , 7 types, 660 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: 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.: 2 / Source method: obtained synthetically / Formula: C24H37N5O2
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 13 / Source method: obtained synthetically
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 631 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG 4000, 20% IProp, 0.1 M NaCitrate pH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 76349 / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.123 / Χ2: 1.505 / Net I/av σ(I): 23.333 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
1.74-1.776.10.8290.85199.4
1.77-1.87.50.8360.8691100
1.8-1.848.20.7760.8731100
1.84-1.878.30.7220.8881100
1.87-1.928.30.6140.9511100
1.92-1.968.30.4641.0161100
1.96-2.018.30.3981.0171100
2.01-2.068.30.3321.0491100
2.06-2.128.30.2841.0791100
2.12-2.198.30.2531.1131100
2.19-2.278.30.2261.2781100
2.27-2.368.30.2111.4541100
2.36-2.478.30.1811.5971100
2.47-2.68.30.151.691100
2.6-2.768.30.1161.6781100
2.76-2.988.30.0941.7031100
2.98-3.278.20.0882.4351100
3.27-3.757.80.0733.0411100
3.75-4.7280.0552.5861100
4.72-507.70.0522.758199.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5TTG

5ttg


Resolution: 1.74→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.112 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 1569 2.1 %RANDOM
Rwork0.1734 ---
obs0.1739 74613 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.38 Å2 / Biso mean: 23.263 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å2-0 Å20 Å2
2---0.97 Å2-0 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 1.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 142 647 4937
Biso mean--25.21 32.96 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194595
X-RAY DIFFRACTIONr_bond_other_d0.0020.024168
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9546244
X-RAY DIFFRACTIONr_angle_other_deg1.0293.0059559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.075564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64722.627236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90215743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0841554
X-RAY DIFFRACTIONr_chiral_restr0.0830.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215410
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021165
X-RAY DIFFRACTIONr_mcbond_it1.2832.162154
X-RAY DIFFRACTIONr_mcbond_other1.2822.162155
X-RAY DIFFRACTIONr_mcangle_it2.093.2262701
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 96 -
Rwork0.258 5437 -
all-5533 -
obs--99.73 %

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