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- EMDB-47355: A focus of tetramer (2) of the cryo-EM structure of human DNMT3A2... -

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Basic information

Entry
Database: EMDB / ID: EMD-47355
TitleA focus of tetramer (2) of the cryo-EM structure of human DNMT3A2-DNMT3B3 complex bound to di-nucleosome
Map data
Sample
  • Complex: DNMT3A/3B tetramer bound to di-nucleosome
    • Protein or peptide: Isoform 3 of DNA (cytosine-5)-methyltransferase 3B
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
KeywordsDNMT3A2 / DNMT3B3 / DNA methylation / di-nucleosome / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / transposable element silencing by piRNA-mediated DNA methylation / protein-cysteine methyltransferase activity / positive regulation of cellular response to hypoxia / DNA-methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / hepatocyte apoptotic process ...DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / transposable element silencing by piRNA-mediated DNA methylation / protein-cysteine methyltransferase activity / positive regulation of cellular response to hypoxia / DNA-methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / hepatocyte apoptotic process / response to vitamin A / XY body / SUMOylation of DNA methylation proteins / DNA methylation-dependent constitutive heterochromatin formation / cellular response to ethanol / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / lncRNA binding / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / response to cocaine / methylation / DNA methylation / PRC2 methylates histones and DNA / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / euchromatin / response to toxic substance / NoRC negatively regulates rRNA expression / response to lead ion / nuclear matrix / RMTs methylate histone arginines / transcription corepressor activity / response to estradiol / neuron differentiation / 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 / chromosome / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
DNA (cytosine-5)-methyltransferase 3B, ADD domain / 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 3B, ADD domain / 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 / Zinc finger, FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 3B / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsXie X / Zhou XE / Worden EJ / Jones PA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA209859 United States
CitationJournal: Mol Cell / Year: 2026
Title: Nucleosome spacing regulates linker methylation by DNMT3A2/3B3.
Authors: Xiaoyan Xie / Minmin Liu / Gabriella N L Chua / X Edward Zhou / Michelle L Dykstra / Shixin Liu / Peter A Jones / Evan J Worden /
Abstract: De novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get ...De novo CpG methylation (mCpG) is deposited by DNMT3A and DNMT3B, which target DNA linkers between nucleosomes. Cells contain millions of unique linkers, but the rules dictating which linkers get targeted by DNMT3 enzymes are not understood. We show that nucleosome spacing controls linker DNA methylation and H3K36me2 recognition by human DNMT3A2/3B3, linking de novo methylation to chromatin architecture. We present structures of DNMT3A2/3B3 bound to dinucleosomes, revealing that short linkers promote dinucleosome bridging, blocking access to linker DNA and suppressing methylation, whereas long linkers allow DNMT3A2/3B3 to engage each nucleosome separately and methylate linker DNA. Finally, we show that DNMT3A2/3B3 positions proline-tryptophan-tryptophan-proline (PWWP) domains to scan for H3K36me2. However, H3K36me2 recognition is blocked when DNMT3A2/3B3 bridges dinucleosomes with short linkers, imposing an additional structural constraint on DNMT3A2/3B3 function. Together, these findings uncover the mechanisms that govern de novo methylation in chromatin and explain how DNMT3 enzymes target linkers in cells.
History
DepositionOct 17, 2024-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47355.png

Downloads & links

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Map

FileDownload / File: emd_47355.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 397.44 Å		0.83 Å/pix.
x 480 pix.
= 397.44 Å		0.83 Å/pix.
x 480 pix.
= 397.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036
Minimum - Maximum-0.0017011943 - 4.660378
Average (Standard dev.)0.0002914069 (±0.012666284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 397.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_47355_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47355_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : DNMT3A/3B tetramer bound to di-nucleosome

EntireName: DNMT3A/3B tetramer bound to di-nucleosome
Components
  • Complex: DNMT3A/3B tetramer bound to di-nucleosome
    • Protein or peptide: Isoform 3 of DNA (cytosine-5)-methyltransferase 3B
    • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: DNMT3A/3B tetramer bound to di-nucleosome

SupramoleculeName: DNMT3A/3B tetramer bound to di-nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Isoform 3 of DNA (cytosine-5)-methyltransferase 3B / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.702383 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MKGDTRHLNG EEDAGGREDS ILVNGACSDQ SSDSPPILEA IRTPEIRGRR SSSRLSKREV SSLLSYTQDL TGDGDGEDGD GSDTPVMPK LFRETRTRSE SPAVRTRNNN SVSSRERHRP SPRSTRGRQG RNHVDESPVE FPATRSLRRR ATASAGTPWP S PPSSYLTI ...String:
MKGDTRHLNG EEDAGGREDS ILVNGACSDQ SSDSPPILEA IRTPEIRGRR SSSRLSKREV SSLLSYTQDL TGDGDGEDGD GSDTPVMPK LFRETRTRSE SPAVRTRNNN SVSSRERHRP SPRSTRGRQG RNHVDESPVE FPATRSLRRR ATASAGTPWP S PPSSYLTI DLTDDTEDTH GTPQSSSTPY ARLAQDSQQG GMESPQVEAD SGDGDSSEYQ DGKEFGIGDL VWGKIKGFSW WP AMVVSWK ATSKRQAMSG MRWVQWFGDG KFSEVSADKL VALGLFSQHF NLATFNKLVS YRKAMYHALE KARVRAGKTF PSS PGDSLE DQLKPMLEWA HGGFKPTGIE GLKPNNTQPE NKTRRRTADD SATSDYCPAP KRLKTNCYNN GKDRGDEKDY DQSR EQMAS DVANNKSSLE DGCLSCGRKN PVSFHPLFEG GLCQTCRDRF LELFYMYDDD GYQSYCTVCC EGRELLLCSN TSCCR CFCV ECLEVLVGTG TAAEAKLQEP WSCYMCLPQR CHGVLRRRKD WNVRLQAFFT SDTGLEYEAP KLYPAIPAAR RRPIRV LSL FDGIATGYLV LKELGIKVGK YVASEVCEES IAVGTVKHEG NIKYVNDVRN ITKKNIEEWG PFDLVIGGSP CNDLSNV NP ARKGLYEGTG RLFFEFYHLL NYSRPKEGDD RPFFWMFENV VAMKVGDKRD ISRFLECNPV MIDAIKVSAA HRARYFWG N LPGMNRIFGF PVHYTDVSNM GRGARQKLLG RSWSVPVIRH LFAPLKDYFA CE

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

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Macromolecule #2: DNA (cytosine-5)-methyltransferase 3A

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA (cytosine-5-)-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.914711 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MNAVEENQGP GESQKVEEAS PPAVQQPTDP ASPTVATTPE PVGSDAGDKN ATKAGDDEPE YEDGRGFGIG ELVWGKLRGF SWWPGRIVS WWMTGRSRAA EGTRWVMWFG DGKFSVVCVE KLMPLSSFCS AFHQATYNKQ PMYRKAIYEV LQVASSRAGK L FPVCHDSD ...String:
MNAVEENQGP GESQKVEEAS PPAVQQPTDP ASPTVATTPE PVGSDAGDKN ATKAGDDEPE YEDGRGFGIG ELVWGKLRGF SWWPGRIVS WWMTGRSRAA EGTRWVMWFG DGKFSVVCVE KLMPLSSFCS AFHQATYNKQ PMYRKAIYEV LQVASSRAGK L FPVCHDSD ESDTAKAVEV QNKPMIEWAL GGFQPSGPKG LEPPEEEKNP YKEVYTDMWV EPEAAAYAPP PPAKKPRKST AE KPKVKEI IDERTRERLV YEVRQKCRNI EDICISCGSL NVTLEHPLFV GGMCQNCKNC FLECAYQYDD DGYQSYCTIC CGG REVLMC GNNNCCRCFC VECVDLLVGP GAAQAAIKED PWNCYMCGHK GTYGLLRRRE DWPSRLQMFF ANNHDQEFDP PKVY PPVPA EKRKPIRVLS LFDGIATGLL VLKDLGIQVD RYIASEVCED SITVGMVRHQ GKIMYVGDVR SVTQKHIQEW GPFDL VIGG SPCNDLSIVN PARKGLYEGT GRLFFEFYRL LHDARPKEGD DRPFFWLFEN VVAMGVSDKR DISRFLESNP VMIDAK EVS AAHRARYFWG NLPGMNRPLA STVNDKLELQ ECLEHGRIAK FSKVRTITTR SNSIKQGKDQ HFPVFMNEKE DILWCTE ME RVFGFPVHYT DVSNMSRLAR QRLLGRSWSV PVIRHLFAPL KEYFACV

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

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 9 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 4 / Number of copies: 2 / 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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6p7a

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211221
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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