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- PDB-9mpp: The cryo-EM structure of nucleosome-bound DNA methyltransferases ... -

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Basic information

Entry
Database: PDB / ID: 9mpp
TitleThe cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L
Components
  • (DNA (167-MER)) x 2
  • (DNA (cytosine-5)-methyltransferase ...) x 2
  • Histone H2A type 1
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsDNA BINDING PROTEIN / methyltransferase / DNMT-nucleosome complex / TRANSFERASE / TRANSFERASE-DNA complex
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 / response to ionizing radiation / DNA methylation-dependent constitutive heterochromatin formation / 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 / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cellular response to amino acid stimulus / enzyme activator activity / euchromatin / response to toxic substance / response to lead ion / RMTs methylate histone arginines / nuclear matrix / neuron differentiation / structural constituent of chromatin / transcription corepressor activity / nucleosome / response to estradiol / 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 / cytosol / 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 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 / Histone-fold / Zinc finger, RING/FYVE/PHD-type / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / DNA (> 100) / 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)
synthetic construct (others)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYan, Y. / Zhou, X.E. / Xu, T.H.
Funding support United States, 2items
OrganizationGrant numberCountry
Other privateStartup Funds
National Institutes of Health/National Cancer Institute (NIH/NCI)R35CA209859 United States
CitationJournal: To Be Published
Title: Structural Insights into DNMT3A-3L-Mediated de novo DNA Methylation on Chromatin
Authors: Yan, Y. / Zhou, X.E. / Thomas, T. / Liu, M. / O'Leary, T. / Griffin, P.R. / Lai, G. / Worden, E. / Jones, P.A. / Xu, T.H.
History
DepositionDec 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B 1.1
I: DNA (167-MER)
J: DNA (167-MER)
M: DNA (cytosine-5)-methyltransferase 3A
N: DNA (cytosine-5)-methyltransferase 3-like
K: DNA (cytosine-5)-methyltransferase 3A
L: DNA (cytosine-5)-methyltransferase 3-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,83922
Polymers454,67714
Non-polymers1,1618
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2 / Histone H3


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 13978.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (167-MER)


Mass: 51327.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (167-MER)


Mass: 51785.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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DNA (cytosine-5)-methyltransferase ... , 2 types, 4 molecules MKNL

#7: Protein DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / DNA methyltransferase HsaIIIA / M.HsaIIIA


Mass: 77914.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3A / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase
#8: Protein DNA (cytosine-5)-methyltransferase 3-like


Mass: 43534.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNMT3L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UJW3

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Non-polymers , 2 types, 8 molecules

#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3LCOMPLEX#1-#80MULTIPLE SOURCES
2NucleosomeCOMPLEX#1-#61RECOMBINANT
3human DNA methyltransferase 3A2 and 3L complexCOMPLEX#7-#81RECOMBINANT
Molecular weightValue: 0.454 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Xenopus laevis (African clawed frog)8355
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 8
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 31987

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
2SerialEMimage acquisition
4cryoSPARC4.6CTF correction
7UCSF Chimerav1.18model fitting
8PHENIXmodel fitting
10cryoSPARC4.6initial Euler assignment
11cryoSPARC4.6final Euler assignment
13cryoSPARC4.63D reconstruction
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10464848
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 625915 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeSource nameType
16pa7

6pa7

16pa7PDBexperimental model
24u7p

4u7p

14u7pPDBexperimental model
31AlphaFoldin silico model
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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