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- PDB-8uw1: Cryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome -

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Basic information

Entry
Database: PDB / ID: 8uw1
TitleCryo-EM structure of DNMT3A1 UDR in complex with H2AK119Ub-nucleosome
Components
  • (DNA (146-MER)) x 2
  • DNA (cytosine-5)-methyltransferase 3A
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsGENE REGULATION / DNMT3A1 / Chromatin / H2A lysine 119 monoubiquitination / DNA Methyltransferase
Function / homology
Function and homology information


positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / 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 / SUMOylation of DNA methylation proteins ...positive regulation of cellular response to hypoxia / transposable element silencing by piRNA-mediated DNA methylation / 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 / SUMOylation of DNA methylation proteins / 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 / cellular response to ethanol / chromosome, centromeric region / catalytic complex / heterochromatin / Transferases; Transferring one-carbon groups; Methyltransferases / DNA methylation / PRC2 methylates histones and DNA / post-embryonic development / Defective pyroptosis / response to cocaine / cellular response to amino acid stimulus / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / 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 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 / 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 / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H4 / Histone H2B 1.1 / Histone H3.2 / Histone H2A / DNA (cytosine-5)-methyltransferase 3A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Escherichia coli 'BL21-GoldpLysS AG'
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsGretarsson, K. / Abini-Agbomson, S. / Armache, K.-J. / Lu, C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115882 United States
The Mark Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM088118 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA266978 United States
CitationJournal: Sci Adv / Year: 2024
Title: Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch.
Authors: Kristjan H Gretarsson / Stephen Abini-Agbomson / Susan L Gloor / Daniel N Weinberg / Jamie L McCuiston / Vishnu Udayakumar Sunitha Kumary / Allison R Hickman / Varun Sahu / Rachel Lee / ...Authors: Kristjan H Gretarsson / Stephen Abini-Agbomson / Susan L Gloor / Daniel N Weinberg / Jamie L McCuiston / Vishnu Udayakumar Sunitha Kumary / Allison R Hickman / Varun Sahu / Rachel Lee / Xinjing Xu / Natalie Lipieta / Samuel Flashner / Oluwatobi A Adeleke / Irina K Popova / Hailey F Taylor / Kelsey Noll / Carolina Lin Windham / Danielle N Maryanski / Bryan J Venters / Hiroshi Nakagawa / Michael-Christopher Keogh / Karim-Jean Armache / Chao Lu /
Abstract: During tumor development, promoter CpG islands that are normally silenced by Polycomb repressive complexes (PRCs) become DNA-hypermethylated. The molecular mechanism by which de novo DNA ...During tumor development, promoter CpG islands that are normally silenced by Polycomb repressive complexes (PRCs) become DNA-hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) [DNMT(s)] catalyze CpG methylation at PRC-regulated regions remains unclear. Here, we report a cryo-electron microscopy structure of the DNMT3A long isoform (DNMT3A1) amino-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine-119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 amino terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Further, aberrant redistribution of DNMT3A1 to Polycomb target genes recapitulates the cancer-associated DNA hypermethylation signature and inhibits their transcriptional activation during cell differentiation. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for mediating promoter CpG island DNA hypermethylation, a major molecular hallmark of cancer.
History
DepositionNov 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 11, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 21, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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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
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
K: DNA (cytosine-5)-methyltransferase 3A
I: DNA (146-MER)
J: DNA (146-MER)


Theoretical massNumber of molelcules
Total (without water)208,96611
Polymers208,96611
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3.2 / Histone H3


Mass: 15421.101 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
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) / Gene: LOC121398084
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A8J1LTD2
#3: Protein Histone H2A


Mass: 14109.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h2ac14.L
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13979.291 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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P02281
#5: Protein DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / Cysteine methyltransferase DNMT3A / DNA methyltransferase HsaIIIA / DNA MTase HsaIIIA / M.HsaIIIA


Mass: 9028.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9Y6K1, DNA (cytosine-5-)-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases

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DNA chain , 2 types, 2 molecules IJ

#6: DNA chain DNA (146-MER)


Mass: 44824.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#7: DNA chain DNA (146-MER)


Mass: 45304.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Details

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

ComponentName: DNMT3A1 UDR in complex with H2AK119Ub-nucleosome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.9 / Details: 50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMSodium chlorideNaCl1
250 mMHEPESC8H18N2O4S1
32 mMDTTC4H10O2S21
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.1.1particle selection
2Leginonimage acquisition
8PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2896025
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55652 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00713017
ELECTRON MICROSCOPYf_angle_d0.67218836
ELECTRON MICROSCOPYf_dihedral_angle_d30.9033818
ELECTRON MICROSCOPYf_chiral_restr0.0412147
ELECTRON MICROSCOPYf_plane_restr0.0041378

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