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- PDB-5ttf: Crystal structure of catalytic domain of G9a with MS012 -

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Basic information

Entry
Database: PDB / ID: 5ttf
TitleCrystal structure of catalytic domain of G9a with MS012
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE / EHMT2 / G9a / BAT8 / methyltransferase / UNC3832 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly ...histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / C2H2 zinc finger domain binding / protein-lysine N-methyltransferase activity / fertilization / cellular response to cocaine / organ growth / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / Transcriptional Regulation by E2F6 / regulation of DNA replication / RNA Polymerase I Transcription Initiation / Transcriptional Regulation by VENTX / spermatid development / behavioral response to cocaine / Transferases; Transferring one-carbon groups; Methyltransferases / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / cellular response to starvation / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / Senescence-Associated Secretory Phenotype (SASP) / 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 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-7KZ / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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: 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 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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)134,87934
Polymers130,4204
Non-polymers4,45930
Water10,557586
1
A: Histone-lysine N-methyltransferase EHMT2
C: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,43917
Polymers65,2102
Non-polymers2,23015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-8 kcal/mol
Surface area23940 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase EHMT2
D: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,43917
Polymers65,2102
Non-polymers2,23015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-15 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.846, 67.749, 77.845
Angle α, β, γ (deg.)92.090, 90.050, 91.800
Int Tables number1
Space group name H-MP1

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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: UNP residues 879-1159
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, 616 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-7KZ / N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine / N~2~-hexyl-6,7-dimethoxy-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine


Mass: 401.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H35N5O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
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: 1.72→50 Å / Num. obs: 119007 / % possible obs: 96.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.049 / Rrim(I) all: 0.09 / Χ2: 1.67 / Net I/av σ(I): 23.91 / Net I/σ(I): 9.4 / Num. measured all: 372722
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.72-1.752.50.550.82183.5
1.75-1.782.70.4860.818194.4
1.78-1.8230.4330.898195.6
1.82-1.853.20.4070.898196.1
1.85-1.893.20.3360.917196.2
1.89-1.943.20.2760.948196.4
1.94-1.993.20.2230.962196.5
1.99-2.043.20.1830.979196.8
2.04-2.13.20.160.98196.9
2.1-2.173.20.1380.984197.1
2.17-2.243.20.1190.987197.3
2.24-2.333.20.1090.988197.5
2.33-2.443.20.0980.989197.7
2.44-2.573.20.0890.991197.8
2.57-2.733.20.0760.993198.1
2.73-2.943.20.070.995198.2
2.94-3.243.20.0640.993198.3
3.24-3.713.10.0560.994198.5
3.71-4.6730.050.995198.3
4.67-503.10.050.996197.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K5K

3k5k


Resolution: 1.72→50.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.273 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1275 1.1 %RANDOM
Rwork0.2066 ---
obs0.207 117616 96.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.27 Å2 / Biso mean: 28.993 Å2 / Biso min: 8.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.34 Å2-1.4 Å20.33 Å2
2--0.18 Å2-0.35 Å2
3---2.27 Å2
Refinement stepCycle: final / Resolution: 1.72→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8325 0 226 588 9139
Biso mean--30.58 32.35 -
Num. residues----1059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198902
X-RAY DIFFRACTIONr_bond_other_d0.0020.028013
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.95412070
X-RAY DIFFRACTIONr_angle_other_deg1.043.00618326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86451087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.16723.333432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.204151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2781579
X-RAY DIFFRACTIONr_chiral_restr0.0850.21288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210434
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022180
X-RAY DIFFRACTIONr_mcbond_it1.6222.8594277
X-RAY DIFFRACTIONr_mcbond_other1.6222.8594277
X-RAY DIFFRACTIONr_mcangle_it2.4984.2755336
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 85 -
Rwork0.297 7859 -
all-7944 -
obs--87.37 %

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