[English] 日本語
Yorodumi
- EMDB-28158: Cryo-EM structure of human DNMT3B homo-trimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28158
TitleCryo-EM structure of human DNMT3B homo-trimer
Map datasharpened map
Sample
  • Complex: DNA (cytosine-5)-methyltransferase 3B
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3B
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION
KeywordsDNA Methyltransferase / TRANSFERASE
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / : / DNA-methyltransferase activity / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / 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 / DNA (cytosine-5-)-methyltransferase activity / SUMOylation of DNA methylation proteins / : / catalytic complex / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / NoRC negatively regulates rRNA expression / transcription corepressor activity / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3B, ADD domain / : / DNMT3, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / 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, ADD PHD zinc finger / DNMT3, cysteine rich ADD domain / Cysteine rich ADD domain in DNMT3 / 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
DNA (cytosine-5)-methyltransferase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsLu JW / Song JK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Structural basis for the allosteric regulation and dynamic assembly of DNMT3B.
Authors: Jiuwei Lu / Jian Fang / Hongtao Zhu / Kimberly Lu Liang / Nelli Khudaverdyan / Jikui Song /
Abstract: Oligomerization of DNMT3B, a mammalian de novo DNA methyltransferase, critically regulates its chromatin targeting and DNA methylation activities. However, how the N-terminal PWWP and ADD domains ...Oligomerization of DNMT3B, a mammalian de novo DNA methyltransferase, critically regulates its chromatin targeting and DNA methylation activities. However, how the N-terminal PWWP and ADD domains interplay with the C-terminal methyltransferase (MTase) domain in regulating the dynamic assembly of DNMT3B remains unclear. Here, we report the cryo-EM structure of DNMT3B under various oligomerization states. The ADD domain of DNMT3B interacts with the MTase domain to form an autoinhibitory conformation, resembling the previously observed DNMT3A autoinhibition. Our combined structural and biochemical study further identifies a role for the PWWP domain and its associated ICF mutation in the allosteric regulation of DNMT3B tetramer, and a differential functional impact on DNMT3B by potential ADD-H3K4me0 and PWWP-H3K36me3 bindings. In addition, our comparative structural analysis reveals a coupling between DNMT3B oligomerization and folding of its substrate-binding sites. Together, this study provides mechanistic insights into the allosteric regulation and dynamic assembly of DNMT3B.
History
DepositionSep 15, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28158.png

Downloads & links

-
Map

FileDownload / File: emd_28158.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.2399812 - 2.0565286
Average (Standard dev.)0.00011789606 (±0.022970354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_28158_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1

Fileemd_28158_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2

Fileemd_28158_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : DNA (cytosine-5)-methyltransferase 3B

EntireName: DNA (cytosine-5)-methyltransferase 3B
Components
  • Complex: DNA (cytosine-5)-methyltransferase 3B
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3B
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
  • Ligand: ZINC ION

-
Supramolecule #1: DNA (cytosine-5)-methyltransferase 3B

SupramoleculeName: DNA (cytosine-5)-methyltransferase 3B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: DNA (cytosine-5)-methyltransferase 3B

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 73.654023 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GSEADSGDGD SSEYQDGKEF GIGDLVWGKI KGFSWWPAMV VSWKATSKRQ AMSGMRWVQW FGDGKFSEVS ADKLVALGLF SQHFNLATF NKLVSYRKAM YHALEKARVR AGKTFPSSPG DSLEDQLKPM LEWAHGGFKP TGIEGLKPNN TQPVVNKSKV R RAGSRKLE ...String:
GSEADSGDGD SSEYQDGKEF GIGDLVWGKI KGFSWWPAMV VSWKATSKRQ AMSGMRWVQW FGDGKFSEVS ADKLVALGLF SQHFNLATF NKLVSYRKAM YHALEKARVR AGKTFPSSPG DSLEDQLKPM LEWAHGGFKP TGIEGLKPNN TQPVVNKSKV R RAGSRKLE SRKYENKTRR RTADDSATSD YCPAPKRLKT NCYNNGKDRG DEDQSREQMA SDVANNKSSL EDGCLSCGRK NP VSFHPLF EGGLCQTCRD RFLELFYMYD DDGYQSYCTV CCEGRELLLC SNTSCCRCFC VECLEVLVGT GTAAEAKLQE PWS CYMCLP QRCHGVLRRR KDWNVRLQAF FTSDTGLEYE APKLYPAIPA ARRRPIRVLS LFDGIATGYL VLKELGIKVG KYVA SEVCE ESIAVGTVKH EGNIKYVNDV RNITKKNIEE WGPFDLVIGG SPCNDLSNVN PARKGLYEGT GRLFFEFYHL LNYSR PKEG DDRPFFWMFE NVVAMKVGDK RDISRFLECN PVMIDAIKVS AAHRARYFWG NLPGMNRPVI ASKNDKLELQ DCLEYN RIA KLKKVQTITT KSNSIKQGKN QLFPVVMNGK EDVLWCTELE RIFGFPVHYT DVSNMGRGAR QKLLGRSWSV PVIRHLF AP LKDYFACE

UniProtKB: DNA (cytosine-5)-methyltransferase 3B

-
Macromolecule #2: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 2 / Number of copies: 2 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -2.1 µm / Nominal defocus min: -1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 130219

+
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