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- PDB-8xpt: The Crystal Structure of EHMT1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8xpt
TitleThe Crystal Structure of EHMT1 from Biortus.
ComponentsHistone-lysine N-methyltransferase EHMT1
KeywordsTRANSFERASE / Chromatin regulator / Methyltransferase / Metal-binding
Function / homology
Function and homology information


[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / DNA methylation-dependent constitutive heterochromatin formation / Transcriptional Regulation by E2F6 ...[histone H3]-lysine9 N-methyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / DNA methylation-dependent constitutive heterochromatin formation / Transcriptional Regulation by E2F6 / regulation of embryonic development / Transcriptional Regulation by VENTX / response to fungicide / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / transcription corepressor binding / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / positive regulation of cold-induced thermogenesis / chromatin organization / 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 motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / Ankyrin repeats (many copies) / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain ...Histone-lysine N-methyltransferase EHMT1 / 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 / Ankyrin repeats (many copies) / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Bao, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of EHMT1 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Bao, C.
History
DepositionJan 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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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
C: Histone-lysine N-methyltransferase EHMT1
D: Histone-lysine N-methyltransferase EHMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,28928
Polymers131,3214
Non-polymers2,96824
Water52229
1
A: Histone-lysine N-methyltransferase EHMT1
C: Histone-lysine N-methyltransferase EHMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,04913
Polymers65,6602
Non-polymers1,38811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-21 kcal/mol
Surface area24730 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase EHMT1
D: Histone-lysine N-methyltransferase EHMT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,24115
Polymers65,6602
Non-polymers1,58013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-46 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.113, 94.638, 88.731
Angle α, β, γ (deg.)90.000, 112.337, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A
74A
84A
95A
105A
116A
126A

NCS domain segments:

End auth comp-ID: SER / End label comp-ID: SER / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth seq-IDLabel seq-ID
111GLUGLU1007 - 126626 - 285
211GLUGLU1007 - 126626 - 285
322ILEILE1009 - 126628 - 285
422ILEILE1009 - 126628 - 285
533GLUGLU1007 - 126626 - 285
633GLUGLU1007 - 126626 - 285
744ILEILE1009 - 126628 - 285
844ILEILE1009 - 126628 - 285
955GLUGLU1007 - 126626 - 285
1055GLUGLU1007 - 126626 - 285
1166ILEILE1009 - 126628 - 285
1266ILEILE1009 - 126628 - 285

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Histone-lysine N-methyltransferase EHMT1 / Euchromatic histone-lysine N-methyltransferase 1 / Eu-HMTase1 / G9a-like protein 1 / GLP / GLP1 / ...Euchromatic histone-lysine N-methyltransferase 1 / Eu-HMTase1 / G9a-like protein 1 / GLP / GLP1 / Histone H3-K9 methyltransferase 5 / H3-K9-HMTase 5 / Lysine N-methyltransferase 1D


Mass: 32830.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H9B1, Transferases; Transferring one-carbon groups; Methyltransferases, [histone H3]-lysine9 N-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 25% PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95355 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95355 Å / Relative weight: 1
ReflectionResolution: 3.35→48.415 Å / Num. obs: 16513 / % possible obs: 88 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.256 / Net I/σ(I): 5.9
Reflection shellResolution: 3.35→3.62 Å / Rmerge(I) obs: 0.832 / Num. unique obs: 3495

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→48.415 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.867 / SU B: 37.385 / SU ML: 0.558 / Cross valid method: FREE R-VALUE / ESU R Free: 0.68
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2623 798 4.837 %
Rwork0.1953 15701 -
all0.198 --
obs-16499 87.264 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 80.887 Å2
Baniso -1Baniso -2Baniso -3
1-3.757 Å2-0 Å24.002 Å2
2---6.696 Å2-0 Å2
3----0.261 Å2
Refinement stepCycle: LAST / Resolution: 3.35→48.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8131 0 140 29 8300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0128513
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167644
X-RAY DIFFRACTIONr_angle_refined_deg1.0861.66911507
X-RAY DIFFRACTIONr_angle_other_deg0.3591.58517504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59551000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.182596
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg2.1654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.423101366
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg9.0531050
X-RAY DIFFRACTIONr_dihedral_angle_6_deg11.74310450
X-RAY DIFFRACTIONr_chiral_restr0.0480.21190
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022165
X-RAY DIFFRACTIONr_nbd_refined0.2040.21506
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.27680
X-RAY DIFFRACTIONr_nbtor_refined0.180.24137
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2198
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.214
X-RAY DIFFRACTIONr_nbd_other0.2490.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3960.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0510.21
X-RAY DIFFRACTIONr_mcbond_it4.8717.9764039
X-RAY DIFFRACTIONr_mcbond_other4.8717.9764039
X-RAY DIFFRACTIONr_mcangle_it8.01214.3125026
X-RAY DIFFRACTIONr_mcangle_other8.01114.3135027
X-RAY DIFFRACTIONr_scbond_it4.9138.4234474
X-RAY DIFFRACTIONr_scbond_other4.98.4054458
X-RAY DIFFRACTIONr_scangle_it8.05215.3536481
X-RAY DIFFRACTIONr_scangle_other8.03615.3236458
X-RAY DIFFRACTIONr_lrange_it14.03596.85633676
X-RAY DIFFRACTIONr_lrange_other14.03596.8633677
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.057839
X-RAY DIFFRACTIONr_ncsr_local_group_20.0940.057945
X-RAY DIFFRACTIONr_ncsr_local_group_30.0820.057746
X-RAY DIFFRACTIONr_ncsr_local_group_40.0840.057751
X-RAY DIFFRACTIONr_ncsr_local_group_50.0870.057815
X-RAY DIFFRACTIONr_ncsr_local_group_60.0770.057739
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.09130.05011
12AX-RAY DIFFRACTIONLocal ncs0.09130.05011
23AX-RAY DIFFRACTIONLocal ncs0.094230.0501
24AX-RAY DIFFRACTIONLocal ncs0.094230.0501
35AX-RAY DIFFRACTIONLocal ncs0.081650.05011
36AX-RAY DIFFRACTIONLocal ncs0.081650.05011
47AX-RAY DIFFRACTIONLocal ncs0.083780.05011
48AX-RAY DIFFRACTIONLocal ncs0.083780.05011
59AX-RAY DIFFRACTIONLocal ncs0.086940.05011
510AX-RAY DIFFRACTIONLocal ncs0.086940.05011
611AX-RAY DIFFRACTIONLocal ncs0.076560.05011
612AX-RAY DIFFRACTIONLocal ncs0.076560.05011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.35-3.4370.326730.33711830.33713870.9050.90290.55520.306
3.437-3.530.408520.31111720.31513650.8630.92189.67030.285
3.53-3.6320.411380.2711190.27412820.9110.94390.24960.236
3.632-3.7430.293550.23810970.24112840.9390.95189.71960.197
3.743-3.8650.256640.21410470.21612620.9510.96588.03490.176
3.865-40.277470.2129740.21511610.9540.96787.94140.174
4-4.150.324480.1959450.20111500.9290.97486.34780.164
4.15-4.3180.213460.1859040.18611250.970.97684.44440.15
4.318-4.5080.197240.1589060.15910700.9740.98386.91590.132
4.508-4.7260.214390.1578490.1610250.9650.98386.63410.128
4.726-4.9790.214470.1478020.1519750.9690.98687.07690.115
4.979-5.2780.253370.1497330.1549170.9610.98783.96950.124
5.278-5.6380.219420.1516990.1548710.9670.98685.07460.125
5.638-6.0820.22390.1576670.1618140.9740.98586.73220.132
6.082-6.6520.278230.1496290.1547430.950.98687.75240.123
6.652-7.420.273280.1425660.1486830.9530.98686.96930.121
7.42-8.5350.244440.1634730.1696100.9740.98584.75410.149
8.535-10.3730.31180.1684180.1745110.9420.98585.32290.164
10.373-14.3440.222230.23230.2014140.9640.9883.57490.195
14.344-48.4150.176110.2131950.212520.9780.97881.7460.21

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