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- PDB-3swc: GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide -

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Basic information

Entry
Database: PDB / ID: 3swc
TitleGLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide
Components
  • DNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5)-methyltransferase 3A
  • Histone-lysine N-methyltransferase EHMT1
KeywordsTRANSFERASE / epigenetics / non-histone lysine methylation / SET domain / protein lysine methyltransferase
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / : / positive regulation of cellular response to hypoxia / : / PRC2 methylates histones and DNA / epigenetic programming of gene expression / [histone H3]-lysine9 N-methyltransferase / cellular response to bisphenol A / histone H3K27 methyltransferase activity / protein-cysteine methyltransferase activity ...DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / : / positive regulation of cellular response to hypoxia / : / PRC2 methylates histones and DNA / epigenetic programming of gene expression / [histone H3]-lysine9 N-methyltransferase / cellular response to bisphenol A / histone H3K27 methyltransferase activity / protein-cysteine methyltransferase activity / peptidyl-lysine monomethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / RMTs methylate histone arginines / facultative heterochromatin formation / genomic imprinting / DNA (cytosine-5-)-methyltransferase / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / XY body / DNA methylation-dependent heterochromatin formation / protein-lysine N-methyltransferase activity / negative regulation of gene expression via chromosomal CpG island methylation / cellular response to ethanol / C2H2 zinc finger domain binding / response to vitamin A / : / response to ionizing radiation / hepatocyte apoptotic process / Transcriptional Regulation by E2F6 / regulation of embryonic development / chromosome, centromeric region / catalytic complex / Transcriptional Regulation by VENTX / heterochromatin / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / transcription corepressor binding / response to cocaine / methyltransferase activity / cellular response to amino acid stimulus / response to lead ion / euchromatin / Regulation of TP53 Activity through Methylation / neuron differentiation / response to toxic substance / PKMTs methylate histone lysines / nuclear matrix / p53 binding / response to estradiol / chromatin organization / positive regulation of cold-induced thermogenesis / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase EHMT1 / DNA (cytosine-5)-methyltransferase 3A, ADD domain / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / ADD domain ...Histone-lysine N-methyltransferase EHMT1 / DNA (cytosine-5)-methyltransferase 3A, ADD domain / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / ADD domain / ADD domain profile. / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / 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 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Beta Complex / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 3A / Histone-lysine N-methyltransferase EHMT1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.332 Å
AuthorsChang, Y. / Horton, J.R. / Zhang, X. / Cheng, X.
CitationJournal: Nat Commun / Year: 2011
Title: MPP8 mediates the interactions between DNA methyltransferase Dnmt3a and H3K9 methyltransferase GLP/G9a.
Authors: Chang, Y. / Sun, L. / Kokura, K. / Horton, J.R. / Fukuda, M. / Espejo, A. / Izumi, V. / Koomen, J.M. / Bedford, M.T. / Zhang, X. / Shinkai, Y. / Fang, J. / Cheng, X.
History
DepositionJul 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
P: DNA (cytosine-5)-methyltransferase 3A
B: Histone-lysine N-methyltransferase EHMT1
Q: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,52614
Polymers68,2334
Non-polymers1,29210
Water3,063170
1
A: Histone-lysine N-methyltransferase EHMT1
P: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7637
Polymers34,1172
Non-polymers6465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-7 kcal/mol
Surface area13000 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase EHMT1
Q: DNA (cytosine-5)-methyltransferase 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7637
Polymers34,1172
Non-polymers6465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-7 kcal/mol
Surface area12800 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-27 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.09, 90.22, 95.40
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / Fragment: unp residues 982-1266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D / Plasmid: pXC681 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H9B1, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase
#2: Protein/peptide DNA (cytosine-5)-methyltransferase 3A / DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / DNA methyltransferase MmuIIIA / DNA MTase MmuIIIA / M.MmuIIIA


Mass: 1286.509 Da / Num. of mol.: 2 / Fragment: unp residues 39-50 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
References: UniProt: O88508, DNA (cytosine-5-)-methyltransferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.33→40.78 Å / Num. obs: 29318 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 26
Reflection shellResolution: 2.33→2.4 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 5.6 / Num. unique all: 2825 / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3MO5

3mo5


Resolution: 2.332→40.78 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0.04 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1967 6.87 %random
Rwork0.1869 ---
obs0.1897 28620 94.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.413 Å2 / ksol: 0.354 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9521 Å20 Å2-0 Å2
2--5.0336 Å20 Å2
3----5.9857 Å2
Refinement stepCycle: LAST / Resolution: 2.332→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4290 0 60 170 4520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084458
X-RAY DIFFRACTIONf_angle_d1.1376040
X-RAY DIFFRACTIONf_dihedral_angle_d17.5531650
X-RAY DIFFRACTIONf_chiral_restr0.075627
X-RAY DIFFRACTIONf_plane_restr0.005802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.3317-2.4150.3091600.21692184218480
2.415-2.51170.27821860.21052529252991
2.5117-2.6260.23461810.19442544254492
2.626-2.76440.22722020.20232593259394
2.7644-2.93750.27432000.20622688268897
2.9375-3.16430.27112010.20552747274799
3.1643-3.48260.2312130.196327932793100
3.4826-3.98610.21681990.16672812281299
3.9861-5.02060.18432100.150328382838100
5.0206-40.78720.18292150.1742925292598

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