[English] 日本語
Yorodumi
- PDB-7v0e: Crystal structure of the macro-oligomeric form of DNMT3B methyltr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v0e
TitleCrystal structure of the macro-oligomeric form of DNMT3B methyltransferase domain.
ComponentsDNA (cytosine-5)-methyltransferase 3B
KeywordsTRANSFERASE / DNMT3B / DNA methylation / Methyltransferase
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity / DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / DNA (cytosine-5-)-methyltransferase activity, acting on CpNpG substrates / DNA (cytosine-5-)-methyltransferase / SUMOylation of DNA methylation proteins / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / NoRC negatively regulates rRNA expression / transcription corepressor activity / methylation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3B, ADD domain / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / 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. ...DNA (cytosine-5)-methyltransferase 3B, ADD domain / DNMT3, cysteine rich ADD domain / : / DNMT3, cysteine rich ADD domain, GATA1-like zinc finger / DNMT3, ADD PHD zinc finger / ADD domain / ADD domain profile. / 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 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27016388184 Å
AuthorsGao, L. / Lu, J. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R35GM119721 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structure of DNMT3B homo-oligomer reveals vulnerability to impairment by ICF mutations.
Authors: Gao, L. / Guo, Y. / Biswal, M. / Lu, J. / Yin, J. / Fang, J. / Chen, X. / Shao, Z. / Huang, M. / Wang, Y. / Wang, G.G. / Song, J.
History
DepositionMay 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 3B
B: DNA (cytosine-5)-methyltransferase 3B
C: DNA (cytosine-5)-methyltransferase 3B
D: DNA (cytosine-5)-methyltransferase 3B
E: DNA (cytosine-5)-methyltransferase 3B
F: DNA (cytosine-5)-methyltransferase 3B
G: DNA (cytosine-5)-methyltransferase 3B
H: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,32816
Polymers260,2538
Non-polymers3,0758
Water52229
1
A: DNA (cytosine-5)-methyltransferase 3B
D: DNA (cytosine-5)-methyltransferase 3B
E: DNA (cytosine-5)-methyltransferase 3B
F: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6648
Polymers130,1274
Non-polymers1,5384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA (cytosine-5)-methyltransferase 3B
C: DNA (cytosine-5)-methyltransferase 3B
G: DNA (cytosine-5)-methyltransferase 3B
H: DNA (cytosine-5)-methyltransferase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6648
Polymers130,1274
Non-polymers1,5384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.393, 164.393, 209.175
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

-
Components

#1: Protein
DNA (cytosine-5)-methyltransferase 3B / Dnmt3b / DNA methyltransferase HsaIIIB / DNA MTase HsaIIIB / M.HsaIIIB


Mass: 32531.625 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBC3, DNA (cytosine-5-)-methyltransferase
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: 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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.52 Å3/Da / Density % sol: 81.12 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH6.5, 1.4 M Ammonium sulfate, 0.2 mM AdoHcy and 8% v/v 1,4-Dioxane

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9195 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 3.27→142.37 Å / Num. obs: 93113 / % possible obs: 95.3 % / Redundancy: 3 % / Biso Wilson estimate: 77.616004121 Å2 / CC1/2: 0.98 / Net I/σ(I): 8.2
Reflection shellResolution: 3.27→3.33 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.983 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4439 / CC1/2: 0.36 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U8P

6u8p


Resolution: 3.27016388184→84.2879255551 Å / SU ML: 0.442274794998 / Cross valid method: FREE R-VALUE / σ(F): 1.96362416394 / Phase error: 24.7193021628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234582384558 2021 2.17101729509 %
Rwork0.205608383487 91069 -
obs0.206233223941 93090 95.2639227164 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.7766686248 Å2
Refinement stepCycle: LAST / Resolution: 3.27016388184→84.2879255551 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17217 0 0 29 17246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071255778008417640
X-RAY DIFFRACTIONf_angle_d0.86834608048623876
X-RAY DIFFRACTIONf_chiral_restr0.05273399624532600
X-RAY DIFFRACTIONf_plane_restr0.00525328658263040
X-RAY DIFFRACTIONf_dihedral_angle_d20.1074117726458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2702-3.35190.3966561853311310.3407121226686132X-RAY DIFFRACTION89.30557536
3.3519-3.44260.3435880102261560.3089995920566557X-RAY DIFFRACTION97.1209490741
3.4426-3.54390.3556473354071470.2776469405196650X-RAY DIFFRACTION96.9614835949
3.5439-3.65830.2741617892281430.2401908510836647X-RAY DIFFRACTION97.0970970971
3.6583-3.7890.2767251009971500.2371683465286556X-RAY DIFFRACTION96.5864899899
3.789-3.94070.2475528352211380.2149154235896586X-RAY DIFFRACTION96.3185790001
3.9407-4.12010.2541189606291450.1968075899696324X-RAY DIFFRACTION92.2298260622
4.1201-4.33730.2175925132091470.173002163596564X-RAY DIFFRACTION96.658504969
4.3373-4.6090.1825392274141430.1564353256356692X-RAY DIFFRACTION98.1194372667
4.609-4.96480.2044238277431450.1619945124156683X-RAY DIFFRACTION97.4593205824
4.9648-5.46440.2106059510061500.1779280917376268X-RAY DIFFRACTION91.7774917775
5.4644-6.25490.2109216401581460.2109216401586649X-RAY DIFFRACTION97.7838537919
6.2549-7.87960.2085984134361460.2140204613046518X-RAY DIFFRACTION95.118469883
7.8796-84.28792555510.193354051071340.1888512542626243X-RAY DIFFRACTION91.4527463072

+
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