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- PDB-4da4: Structure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA -

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Basic information

Entry
Database: PDB / ID: 4da4
TitleStructure of mouse DNMT1 (731-1602) bound to hemimethylated CpG DNA
Components
  • DNA (cytosine-5)-methyltransferase 1
  • DNA_LOWER_STRAND
  • DNA_UPPER_STRAND
KeywordsTransferase/DNA / Maintenance DNA methylation / Covalent Complex / Transferase-DNA complex
Function / homology
Function and homology information


SUMOylation of DNA methylation proteins / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / : / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / : / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity ...SUMOylation of DNA methylation proteins / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / : / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / : / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / S-adenosylmethionine metabolic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / female germ cell nucleus / methyl-CpG binding / germ cell nucleus / : / heterochromatin / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / replication fork / methyltransferase activity / nuclear estrogen receptor binding / promoter-specific chromatin binding / cellular response to amino acid stimulus / histone deacetylase binding / regulation of cell population proliferation / regulation of gene expression / response to xenobiotic stimulus / protein domain specific binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Bromo adjacent homology (BAH) domain / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DNA Methylase, subunit A, domain 2 / DMAP1-binding domain / DMAP1-binding domain profile. / DNA Methylase; Chain A, domain 2 ...Bromo adjacent homology (BAH) domain / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DNA Methylase, subunit A, domain 2 / DMAP1-binding domain / DMAP1-binding domain profile. / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Vaccinia Virus protein VP39 / SH3 type barrels. / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSong, J. / Patel, D.J.
CitationJournal: Science / Year: 2012
Title: Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation.
Authors: Song, J. / Teplova, M. / Ishibe-Murakami, S. / Patel, D.J.
History
DepositionJan 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: DNA (cytosine-5)-methyltransferase 1
B: DNA (cytosine-5)-methyltransferase 1
C: DNA_UPPER_STRAND
D: DNA_LOWER_STRAND
E: DNA_UPPER_STRAND
F: DNA_LOWER_STRAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,99713
Polymers212,7756
Non-polymers1,2237
Water15,493860
1
A: DNA (cytosine-5)-methyltransferase 1
C: DNA_UPPER_STRAND
D: DNA_LOWER_STRAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9036
Polymers106,3873
Non-polymers5153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6430 Å2
ΔGint-19 kcal/mol
Surface area39090 Å2
MethodPISA
2
B: DNA (cytosine-5)-methyltransferase 1
E: DNA_UPPER_STRAND
F: DNA_LOWER_STRAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0957
Polymers106,3873
Non-polymers7074
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-21 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.680, 152.042, 96.053
Angle α, β, γ (deg.)90.00, 94.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA (cytosine-5)-methyltransferase 1 / Dnmt1 / Met-1 / DNA methyltransferase MmuI / DNA MTase MmuI / M.MmuI / MCMT


Mass: 98980.555 Da / Num. of mol.: 2 / Fragment: UNP residues 731-1602
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt1, Dnmt, Met1, Uim / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
References: UniProt: P13864, DNA (cytosine-5-)-methyltransferase

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA_UPPER_STRAND


Mass: 3678.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized
#3: DNA chain DNA_LOWER_STRAND


Mass: 3728.462 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized

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Non-polymers , 4 types, 867 molecules

#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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 3 mM TCEP, 0.1 M sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2011
RadiationMonochromator: Si mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 78812 / Num. obs: 77126 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -1 / Redundancy: 2.7 % / Rsym value: 0.096 / Net I/σ(I): 12.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.474 / % possible all: 98

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.47 Å / SU ML: 0.82 / σ(F): 1.38 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 3882 5.04 %
Rwork0.196 --
obs0.198 77070 97.8 %
all-78812 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.4 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.3146 Å2-0 Å21.4507 Å2
2---6.5241 Å2-0 Å2
3----5.7905 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13152 978 69 860 15059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614684
X-RAY DIFFRACTIONf_angle_d1.1920142
X-RAY DIFFRACTIONf_dihedral_angle_d17.5345456
X-RAY DIFFRACTIONf_chiral_restr0.0882131
X-RAY DIFFRACTIONf_plane_restr0.0052467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63080.33951360.29972524X-RAY DIFFRACTION95
2.6308-2.66410.35391510.30912588X-RAY DIFFRACTION98
2.6641-2.69910.40051260.28912623X-RAY DIFFRACTION99
2.6991-2.73610.34411430.28972647X-RAY DIFFRACTION98
2.7361-2.77520.34411380.26442596X-RAY DIFFRACTION99
2.7752-2.81660.33741320.26042648X-RAY DIFFRACTION98
2.8166-2.86060.3281470.26022609X-RAY DIFFRACTION99
2.8606-2.90750.29481200.2542659X-RAY DIFFRACTION98
2.9075-2.95760.34511320.24262614X-RAY DIFFRACTION99
2.9576-3.01140.2891440.22052634X-RAY DIFFRACTION99
3.0114-3.06920.29251370.20882610X-RAY DIFFRACTION98
3.0692-3.13190.23181430.20332610X-RAY DIFFRACTION98
3.1319-3.19990.2511480.19982656X-RAY DIFFRACTION99
3.1999-3.27430.21741210.192633X-RAY DIFFRACTION99
3.2743-3.35620.21691180.19312650X-RAY DIFFRACTION99
3.3562-3.44690.27361250.19282652X-RAY DIFFRACTION98
3.4469-3.54820.25371520.19692625X-RAY DIFFRACTION99
3.5482-3.66270.25211480.19462599X-RAY DIFFRACTION98
3.6627-3.79350.23191450.18342633X-RAY DIFFRACTION98
3.7935-3.94530.22881460.16982626X-RAY DIFFRACTION98
3.9453-4.12460.22231420.15232628X-RAY DIFFRACTION98
4.1246-4.34180.18741480.14822611X-RAY DIFFRACTION98
4.3418-4.61350.18791550.14192586X-RAY DIFFRACTION97
4.6135-4.96910.19091260.15022623X-RAY DIFFRACTION97
4.9691-5.46790.22891600.17412561X-RAY DIFFRACTION96
5.4679-6.25650.20781300.19952573X-RAY DIFFRACTION96
6.2565-7.87220.27071460.21362583X-RAY DIFFRACTION96
7.8722-39.4670.18291230.17032587X-RAY DIFFRACTION94

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