[English] 日本語
Yorodumi
- PDB-3av4: Crystal structure of mouse DNA methyltransferase 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3av4
TitleCrystal structure of mouse DNA methyltransferase 1
ComponentsDNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE / CXXC-type zinc finger/C5-methyltransferase family / Methylates CpG residues. Preferentially methylates hemimethylated DNA / DNA binding / hemi-methylation / Nucleus
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 / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process ...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 / DNA-methyltransferase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / 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 / methyltransferase activity / replication fork / promoter-specific chromatin binding / nuclear estrogen receptor 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
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 / DMAP1-binding domain / DMAP1-binding domain profile. / 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 ...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 / DMAP1-binding domain / DMAP1-binding domain profile. / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsTakeshita, K. / Suetake, I. / Yamashita, E. / Suga, M. / Narita, H. / Nakagawa, A. / Tajima, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural insight into maintenance methylation by mouse DNA methyltransferase 1 (Dnmt1).
Authors: Takeshita, K. / Suetake, I. / Yamashita, E. / Suga, M. / Narita, H. / Nakagawa, A. / Tajima, S.
History
DepositionFeb 22, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 27, 2012Group: Experimental preparation
Revision 1.3Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Mar 13, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,0585
Polymers150,7961
Non-polymers2624
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.780, 97.865, 130.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

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


Mass: 150796.469 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 291-1620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt1, Dnmt, Met1, Uim / Plasmid: pFastBacHTb / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P13864, DNA (cytosine-5-)-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.27 % / Mosaicity: 0.564 °
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 9
Details: PEG 3350, NaCl, TCEP, pH 9.0, vapor diffusion, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU
Wavelength: 0.900, 0.97894, 0.97954, 1.2454, 1.28220, 1.28309
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 7, 2010 / Details: mirror
RadiationMonochromator: Si 111 DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.978941
30.979541
41.24541
51.28221
61.283091
ReflectionResolution: 2.75→200 Å / Num. obs: 45792 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 65.7 Å2 / Rmerge(I) obs: 0.077 / Χ2: 1.69 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.75-2.83.80.37222861.0131100
2.8-2.853.80.33322331.0091100
2.85-2.93.80.27622661.0121100
2.9-2.963.80.23822570.9871100
2.96-3.033.80.22122721.0671100
3.03-3.13.80.18322561.0761100
3.1-3.173.80.15422571.1531100
3.17-3.263.80.13223011.161100
3.26-3.363.80.11122431.221100
3.36-3.463.80.09422611.3351100
3.46-3.593.70.08322591.4721100
3.59-3.733.70.07122901.5931100
3.73-3.93.70.06422831.7451100
3.9-4.115.10.07922931.715199.9
4.11-4.377.40.08722871.8461100
4.37-4.77.30.08123082.3651100
4.7-5.187.10.08123122.5791100
5.18-5.927.10.08323192.5991100
5.92-7.467.20.05723581.8581100
7.46-2006.50.03224511.569198.1

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.75→43.42 Å / Cor.coef. Fo:Fc: 0.9117 / Cor.coef. Fo:Fc free: 0.8737 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 2315 5.06 %RANDOM
Rwork0.2297 ---
obs0.2316 45744 --
Displacement parametersBiso max: 170.16 Å2 / Biso mean: 62.23 Å2 / Biso min: 9.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.3372 Å20 Å20 Å2
2---2.6991 Å20 Å2
3---3.0363 Å2
Refine analyzeLuzzati coordinate error obs: 0.496 Å
Refinement stepCycle: LAST / Resolution: 2.75→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9110 0 4 42 9156
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019330HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2712615HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3251SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes240HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1342HARMONIC5
X-RAY DIFFRACTIONt_it9330HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion22.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1166SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10257SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.82 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3635 154 4.84 %
Rwork0.3111 3025 -
all0.3136 3179 -
obs-3179 -
Refinement TLS params.

Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)
10.3210.26570.32220.46470.26050.33560.1425-0.33720.2460.0228-0.26170.38290.1597-0.3050.11920.0226-0.152-0.09090.1435-0.06660.1827
21.92690.92720.78370.59050.41870.23530.0005-0.001-0.02840.02240.01020.0889-0.01810.0143-0.01070.005-0.00750.03250.00940.0107-0.0164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A357 - 1612
2X-RAY DIFFRACTION2A2001 - 2005

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more