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- PDB-23nx: Structure of mouse DNMT3A-TCL1A complex -

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Basic information

Entry
Database: PDB / ID: 23nx
TitleStructure of mouse DNMT3A-TCL1A complex
Components
  • DNA (cytosine-5)-methyltransferase 3A
  • T-cell leukemia/lymphoma protein 1A
KeywordsTRANSFERASE / DNA methyltransferase / complex
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / autosome genomic imprinting / cellular response to bisphenol A / epigenetic programming of gene expression / PRC2 methylates histones and DNA / genomic imprinting / transposable element silencing by piRNA-mediated DNA methylation / RMTs methylate histone arginines / protein-cysteine methyltransferase activity / positive regulation of cellular response to hypoxia ...DNA (cytosine-5-)-methyltransferase activity, acting on CpN substrates / autosome genomic imprinting / cellular response to bisphenol A / epigenetic programming of gene expression / PRC2 methylates histones and DNA / genomic imprinting / transposable element silencing by piRNA-mediated DNA methylation / RMTs methylate histone arginines / 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 / post-embryonic development / XY body / DNA methylation-dependent constitutive heterochromatin formation / activation of protein kinase B activity / negative regulation of gene expression via chromosomal CpG island methylation / response to ionizing radiation / lncRNA binding / catalytic complex / cellular response to ethanol / chromosome, centromeric region / heterochromatin / protein serine/threonine kinase activator activity / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to amino acid stimulus / response to cocaine / euchromatin / response to toxic substance / response to lead ion / nuclear matrix / response to estradiol / neuron differentiation / methylation / heterochromatin formation / spermatogenesis / cellular response to hypoxia / RNA polymerase II-specific DNA-binding transcription factor binding / intracellular signal transduction / 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 / endoplasmic reticulum / DNA binding / DNA-templated transcription / nucleoplasm / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
TCL1/MTCP1 / TCL1/MTCP1 superfamily / TCL1/MTCP1 family / 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 ...TCL1/MTCP1 / TCL1/MTCP1 superfamily / TCL1/MTCP1 family / 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 / T-cell leukemia/lymphoma protein 1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsLi, W. / Liu, Q. / Li, J. / Wang, X. / Guo, L. / He, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2021YFC2701501 China
CitationJournal: J Struct Biol / Year: 2026
Title: Cryo-EM structure of the murine DNMT3A-TCL1A complex.
Authors: Wei Li / Qingting Liu / Jinhong Li / Xiang Wang / Guolin He / Li Guo /
Abstract: DNA methyltransferase DNMT3A is a key enzyme responsible for establishing DNA methylation patterns during mammalian development. T-cell leukemia/lymphoma 1 A (TCL1A) is a proto-oncogene expressed ...DNA methyltransferase DNMT3A is a key enzyme responsible for establishing DNA methylation patterns during mammalian development. T-cell leukemia/lymphoma 1 A (TCL1A) is a proto-oncogene expressed mainly in embryonic and fetal tissues, as well as in specific lymphocyte populations. In this study, we determined the structure of the murine DNMT3A-TCL1A complex using single-particle cryo-electron microscopy. The complex adopts a linear conformation, with two TCL1A dimers bound to the catalytic domain of DNMT3A to form a heterohexamer. TCL1A competitively binds to the same structural interface on DNMT3A as DNMT3L, but produces an inhibitory-rather than an activating-effect on the catalytic activity of DNMT3A. Furthermore, comparative analysis with previously reported assembly modes of murine TCL1A revealed that the TCL1A dimer complex we resolved adopts distinct molecular conformations and interaction mechanisms. Our findings elucidate the allosteric mechanism by which murine TCL1A inhibits DNMT3A activity, providing a structural basis for understanding mammalian epigenetic reprogramming.
History
DepositionFeb 11, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / 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: T-cell leukemia/lymphoma protein 1A
C: T-cell leukemia/lymphoma protein 1A
D: T-cell leukemia/lymphoma protein 1A
E: T-cell leukemia/lymphoma protein 1A
B: DNA (cytosine-5)-methyltransferase 3A
F: DNA (cytosine-5)-methyltransferase 3A


Theoretical massNumber of molelcules
Total (without water)244,0536
Polymers244,0536
Non-polymers00
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

#1: Protein
T-cell leukemia/lymphoma protein 1A / Oncogene TCL-1 / Oncogene TCL1 / Protein p14 TCL1


Mass: 14130.103 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tcl1a, Tcl1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P56280
#2: Protein DNA (cytosine-5)-methyltransferase 3A / Dnmt3a / Cysteine methyltransferase DNMT3A / DNA methyltransferase MmuIIIA / DNA MTase MmuIIIA / M.MmuIIIA


Mass: 93766.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt3a / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O88508, DNA (cytosine-5-)-methyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases
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: DNMT3A-TCL1A complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 1800 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 55.13 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76682 / Symmetry type: POINT
RefinementHighest resolution: 3.32 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00210656
ELECTRON MICROSCOPYf_angle_d0.49114426
ELECTRON MICROSCOPYf_dihedral_angle_d11.9374004
ELECTRON MICROSCOPYf_chiral_restr0.0411505
ELECTRON MICROSCOPYf_plane_restr0.0041869

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