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- EMDB-75877: Cryo-EM structure of human DNMT3A R882H octadecamer -

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Basic information

Entry
Database: EMDB / ID: EMD-75877
TitleCryo-EM structure of human DNMT3A R882H octadecamer
Map datastructure of human DNMT3A R882H octadecamer
Sample
  • Complex: DNA (cytosine-5)-methyltransferase 3A R882H
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordsDNA (cytosine-5)-methyltransferase / TRANSFERASE
Function / homology
Function and homology information


transposable element silencing by piRNA-mediated DNA methylation / protein-cysteine methyltransferase activity / positive regulation of cellular response to hypoxia / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / hepatocyte apoptotic process / response to vitamin A / SUMOylation of DNA methylation proteins ...transposable element silencing by piRNA-mediated DNA methylation / protein-cysteine methyltransferase activity / positive regulation of cellular response to hypoxia / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / hepatocyte apoptotic process / response to vitamin A / SUMOylation of DNA methylation proteins / XY body / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / lncRNA binding / cellular response to ethanol / chromosome, centromeric region / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / PRC2 methylates histones and DNA / response to cocaine / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / euchromatin / response to toxic substance / response to lead ion / nuclear matrix / RMTs methylate histone arginines / transcription corepressor activity / response to estradiol / neuron differentiation / methylation / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / 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 (cytosine-5)-methyltransferase 3A, ADD domain / : / DNA (cytosine-5-)-methyltransferase, N-terminal / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.04 Å
AuthorsSong J / Lu J / Chen J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of human DNMT3A R882H octadecamer
Authors: Song J / Lu J / Chen J
History
DepositionMar 5, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75877.png

Downloads & links

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Map

FileDownload / File: emd_75877.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of human DNMT3A R882H octadecamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 512 pix.
= 693.146 Å		1.35 Å/pix.
x 512 pix.
= 693.146 Å		1.35 Å/pix.
x 512 pix.
= 693.146 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3538 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.769081 - 1.2172986
Average (Standard dev.)-0.00029772223 (±0.018158086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 693.1456 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75877_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_75877_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_75877_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_75877_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA (cytosine-5)-methyltransferase 3A R882H

EntireName: DNA (cytosine-5)-methyltransferase 3A R882H
Components
  • Complex: DNA (cytosine-5)-methyltransferase 3A R882H
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: DNA (cytosine-5)-methyltransferase 3A R882H

SupramoleculeName: DNA (cytosine-5)-methyltransferase 3A R882H / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3A / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 72.27875 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SEPEYEDGRG FGIGELVWGK LRGFSWWPGR IVSWWMTGRS RAAEGTRWVM WFGDGKFSVV CVEKLMPLSS FCSAFHQATY NKQPMYRKA IYEVLQVASS RAGKLFPVCH DSDESDTAKA VEVQNKPMIE WALGGFQPSG PKGLEPPEEE KNPYKEVYTD M WVEPEAAA ...String:
SEPEYEDGRG FGIGELVWGK LRGFSWWPGR IVSWWMTGRS RAAEGTRWVM WFGDGKFSVV CVEKLMPLSS FCSAFHQATY NKQPMYRKA IYEVLQVASS RAGKLFPVCH DSDESDTAKA VEVQNKPMIE WALGGFQPSG PKGLEPPEEE KNPYKEVYTD M WVEPEAAA YAPPPPAKKP RKSTAEKPKV KEIIDERTRE RLVYEVRQKC RNIEDICISC GSLNVTLEHP LFVGGMCQNC KN CFLECAY QYDDDGYQSY CTICCGGREV LMCGNNNCCR CFCVECVDLL VGPGAAQAAI KEDPWNCYMC GHKGTYGLLR RRE DWPSRL QMFFANNHDQ EFDPPKVYPP VPAEKRKPIR VLSLFDGIAT GLLVLKDLGI QVDRYIASEV CEDSITVGMV RHQG KIMYV GDVRSVTQKH IQEWGPFDLV IGGSPCNDLS IVNPARKGLY EGTGRLFFEF YRLLHDARPK EGDDRPFFWL FENVV AMGV SDKRDISRFL ESNPVMIDAK EVSAAHRARY FWGNLPGMNR PLASTVNDKL ELQECLEHGR IAKFSKVRTI TTRSNS IKQ GKDQHFPVFM NEKEDILWCT EMERVFGFPV HYTDVSNMSH LARQRLLGRS WSVPVIRHLF APLKEYFACV

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

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 42 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 3 / Number of copies: 16 / Formula: SAH
Molecular weightTheoretical: 384.411 Da
Chemical component information

ChemComp-SAH:
S-ADENOSYL-L-HOMOCYSTEINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 32187
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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