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- PDB-5ttg: Crystal structure of catalytic domain of GLP with MS012 -

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Basic information

Entry
Database: PDB / ID: 5ttg
TitleCrystal structure of catalytic domain of GLP with MS012
ComponentsHistone-lysine N-methyltransferase EHMT1
KeywordsTRANSFERASE / EHMT1 / GLP / MS012 / 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-7KZ / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 1.0Feb 1, 2017Provider: 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 / _citation_author.name
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 EHMT1
B: Histone-lysine N-methyltransferase EHMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,27832
Polymers65,9492
Non-polymers2,32930
Water11,403633
1
A: Histone-lysine N-methyltransferase EHMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,16415
Polymers32,9741
Non-polymers1,18914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase EHMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,11417
Polymers32,9741
Non-polymers1,14016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.429, 95.900, 102.113
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
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2000
2111B2000

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.31262, -0.626279, -0.714174), (-0.638671, -0.695124, 0.330004), (-0.703113, 0.352956, -0.617295)-36.37682, -26.65601, -43.601681

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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: UNP residues 879-1159
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 (E. coli) / 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 , 8 types, 663 molecules

#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: 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.: 2 / Source method: obtained synthetically / Formula: C22H35N5O2
#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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 15 / Source method: obtained synthetically
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
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: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / 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: 1.66→50 Å / Num. obs: 86624 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.049 / Rrim(I) all: 0.128 / Χ2: 1.76 / Net I/av σ(I): 25.153 / Net I/σ(I): 7.4 / Num. measured all: 591766
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.66-1.696.50.8830.7891100
1.69-1.726.60.810.8151100
1.72-1.756.70.6630.8711100
1.75-1.796.70.5790.9011100
1.79-1.836.70.510.9151100
1.83-1.876.70.4410.9381100
1.87-1.926.80.3690.9591100
1.92-1.976.80.3040.9641100
1.97-2.036.90.2490.9761100
2.03-2.096.90.2250.9791100
2.09-2.1770.1910.9841100
2.17-2.2570.1670.9871100
2.25-2.3670.1480.9891100
2.36-2.4870.1350.9911100
2.48-2.637.10.1150.9931100
2.63-2.847.10.1020.9931100
2.84-3.1270.090.9941100
3.12-3.586.90.0750.9961100
3.58-4.56.70.0670.9961100
4.5-506.60.0740.993199.3

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Processing

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

3k5k


Resolution: 1.66→50.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.66 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 1745 2 %RANDOM
Rwork0.1707 ---
obs0.1711 84739 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.19 Å2 / Biso mean: 21.363 Å2 / Biso min: 11.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0 Å20 Å2
2---0.74 Å20 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 1.66→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 137 645 4904
Biso mean--23.05 32.32 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194621
X-RAY DIFFRACTIONr_bond_other_d0.0020.024190
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.966295
X-RAY DIFFRACTIONr_angle_other_deg1.0423.0059597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.79422.554231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3915741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6381552
X-RAY DIFFRACTIONr_chiral_restr0.0830.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215491
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021179
X-RAY DIFFRACTIONr_mcbond_it1.1722.0072186
X-RAY DIFFRACTIONr_mcbond_other1.1712.0072186
X-RAY DIFFRACTIONr_mcangle_it1.95132750
Refine LS restraints NCSNumber: 48 / Type: TIGHT THERMAL / Rms dev position: 0.85 Å / Weight position: 0.5
LS refinement shellResolution: 1.662→1.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 137 -
Rwork0.235 6144 -
all-6281 -
obs--99.49 %

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