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- EMDB-48498: The cryo-EM structure of nucleosome-bound DNA methyltransferases ... -

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Basic information

Entry
Database: EMDB / ID: EMD-48498
TitleThe cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Map dataComposited map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Sample
  • Complex: Nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
    • Complex: Nucleosome
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
      • DNA: DNA (167-MER)
      • DNA: DNA (167-MER)
    • Complex: human DNA methyltransferase 3A2 and 3L complex
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3-like
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE
Keywordsmethyltransferase / DNMT-nucleosome complex / TRANSFERASE / TRANSFERASE-DNA complex / DNA BINDING PROTEIN
Function / homology
Function and homology information


epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / cellular response to bisphenol A ...epigenetic programing of female pronucleus / chorionic trophoblast cell differentiation / positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / negative regulation of DNA methylation-dependent heterochromatin formation / transposable element silencing by heterochromatin formation / protein-cysteine methyltransferase activity / regulatory ncRNA-mediated heterochromatin formation / unmethylated CpG binding / cellular response to bisphenol A / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / autosome genomic imprinting / genomic imprinting / SUMOylation of DNA methylation proteins / ESC/E(Z) complex / XY body / response to vitamin A / DNA methylation-dependent constitutive heterochromatin formation / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / hepatocyte apoptotic process / lncRNA binding / negative regulation of gene expression, epigenetic / male meiosis I / cellular response to ethanol / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / placenta development / condensed nuclear chromosome / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / response to cocaine / stem cell differentiation / cellular response to amino acid stimulus / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / enzyme activator activity / euchromatin / response to lead ion / response to toxic substance / RMTs methylate histone arginines / nuclear matrix / neuron differentiation / structural constituent of chromatin / transcription corepressor activity / response to estradiol / nucleosome / heterochromatin formation / nucleosome assembly / spermatogenesis / methylation / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
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 methylase, C-5 cytosine-specific, active site ...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 / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / DNA (cytosine-5)-methyltransferase 3-like / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYan Y / Zhou XE / Xu TH / Xu HE / Kossiakoff AA / Melcher K
Funding support United States, 2 items
OrganizationGrant numberCountry
Other privateStartup Funds
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA209859 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Mechanisms of DNMT3A-3L-mediated de novo DNA methylation on chromatin.
Authors: Yan Yan / X Edward Zhou / Stacey L Thomas / Minmin Liu / Gan-Qiang Lai / Evan J Worden / Peter A Jones / Ting-Hai Xu /
Abstract: De novo DNA methylation is mediated by DNA methyltransferases DNMT3A and DNMT3B, in cooperation with the catalytically inactive paralogs DNMT3L and DNMT3B3. DNMT3L is predominantly expressed in ...De novo DNA methylation is mediated by DNA methyltransferases DNMT3A and DNMT3B, in cooperation with the catalytically inactive paralogs DNMT3L and DNMT3B3. DNMT3L is predominantly expressed in embryonic stem cells to establish methylation patterns and is silenced upon differentiation, with DNMT3B3 substituting in somatic cells. Here we present high-resolution cryo-electron microscopy structures of nucleosome-bound, full-length DNMT3A2-3L and its oligomeric assemblies in the nucleosome-free state. We identified the critical role of DNMT3L as a histone modification sensor, guiding chromatin engagement through a mechanism distinct from DNMT3B3. The structures show a 180° rotated 'switching helix' in DNMT3L that prevents direct interaction with the nucleosome acidic patch. Instead, nucleosome binding is mediated by the DNMT3L ADD domain, while the DNMT3A PWWP domain exhibits reduced engagement in the absence of H3K36 methylation. The oligomeric arrangement of DNMT3A2-3L in nucleosome-free states highlights its dynamic assembly and potential allosteric regulation. We further capture dynamic structural movements of DNMT3A2-3L on nucleosomes. These findings uncover a previously unknown mechanism by which DNMT3A-3L mediates de novo DNA methylation on chromatin through complex assembly, histone tail sensing, dynamic DNA search and regulated nucleosome engagement, providing insights into epigenetic regulation.
History
DepositionDec 31, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48498.png

Downloads & links

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Map

FileDownload / File: emd_48498.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposited map of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 Å		0.83 Å/pix.
x 400 pix.
= 331.2 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: 0.02
Minimum - Maximum-0.0013966281 - 1.885943
Average (Standard dev.)0.0011552921 (±0.021781959)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 331.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L

EntireName: Nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Components
  • Complex: Nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
    • Complex: Nucleosome
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
      • DNA: DNA (167-MER)
      • DNA: DNA (167-MER)
    • Complex: human DNA methyltransferase 3A2 and 3L complex
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3A
      • Protein or peptide: DNA (cytosine-5)-methyltransferase 3-like
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYL-L-HOMOCYSTEINE

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Supramolecule #1: Nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L

SupramoleculeName: Nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 454 KDa

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Supramolecule #2: Nucleosome

SupramoleculeName: Nucleosome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: human DNA methyltransferase 3A2 and 3L complex

SupramoleculeName: human DNA methyltransferase 3A2 and 3L complex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: DNA (cytosine-5)-methyltransferase 3A

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3A / type: protein_or_peptide / ID: 7 / 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 frugiperda (fall armyworm)
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 #8: DNA (cytosine-5)-methyltransferase 3-like

MacromoleculeName: DNA (cytosine-5)-methyltransferase 3-like / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.534633 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAITALDPE AEPSMDVILV GSSELSSSVS PGTGRDLIAY EVKANQRNIE DICICCGSLQ VHTQHPLFEG GICAPCKDKF LDALFLYDD DGYQSYCSIC CSGETLLICG NPDCTRCYCF ECVDSLVGPG TSGKVHAMSN WVCYLCLPSS RSGLLQRRRK W RSQLKAFY ...String:
MAAITALDPE AEPSMDVILV GSSELSSSVS PGTGRDLIAY EVKANQRNIE DICICCGSLQ VHTQHPLFEG GICAPCKDKF LDALFLYDD DGYQSYCSIC CSGETLLICG NPDCTRCYCF ECVDSLVGPG TSGKVHAMSN WVCYLCLPSS RSGLLQRRRK W RSQLKAFY DRESENPLEM FETVPVWRRQ PVRVLSLFED IKKELTSLGF LESGSDPGQL KHVVDVTDTV RKDVEEWGPF DL VYGATPP LGHTCDRPPS WYLFQFHRLL QYARPKPGSP GPFFWMFVDN LVLNKEDLDV ASRFLEMEPV TIPDVHGGSL QNA VRVWSN IPAIRSRHWA LVSEEELSLL AQNKQSSKLA AKWPTKLVKN CFLPLREYFK YFSTELTSSL

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

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Macromolecule #5: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.327652 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA) (DT)(DT)(DG)(DG)(DT)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT) (DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC)(DT) (DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG) (DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC) (DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DG)(DC) (DG)(DG) (DC)(DC)(DG)(DA)(DT)

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Macromolecule #6: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 51.785953 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG) (DA)(DG)(DA)(DC)(DT)(DA) ...String:
(DA)(DT)(DC)(DG)(DG)(DC)(DC)(DG)(DC)(DC) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC)(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA)(DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT) (DT)(DG)(DG)(DC)(DG)(DG)(DT) (DT)(DA)(DA)(DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG) (DA)(DC)(DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT)(DA)(DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DT)(DG)(DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG) (DG)(DC)(DA) (DC)(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC)(DT) (DC)(DC)(DA)(DG)(DG)(DG)(DC) (DG)(DG) (DC)(DC)(DG)(DA)(DT)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: S-ADENOSYL-L-HOMOCYSTEINE

MacromoleculeName: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 10 / 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

Concentration0.2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 3 / Number real images: 31987 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10464848
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 625915
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)

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Atomic model buiding 1

Initial model
PDB IDChain

6pa7

source_name: PDB, initial_model_type: experimental model

4u7p

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9mpp:
The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L

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