9LQ1 | pdb_00009lq1

Structure of human DNMT3A-TCL1A complex

• PDB DOI: https://doi.org/10.2210/pdb9LQ1/pdb
• EM Map EMD-63290: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-01-27 Released: 2025-11-05 
• Deposition Author(s): Liu, Q.T., Li, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular basis for inhibition of de novo DNA methylation by TCL1A

Liu, Q.T., Li, J.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 258.29 kDa 
• Atom Count: 10,649 
• Modeled Residue Count: 1,307 
• Deposited Residue Count: 2,280 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 1 of DNA (cytosine-5)-methyltransferase 3A	A, D [auth F]	912	Homo sapiens	Mutation(s): 0  Gene Names: DNMT3A EC: 2.1.1.37 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K1 (Homo sapiens) Explore Q9Y6K1  Go to UniProtKB:  Q9Y6K1
PHAROS:  Q9Y6K1 GTEx:  ENSG00000119772

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell leukemia/lymphoma protein 1A	B, C [auth E], E [auth D], F [auth C]	114	Homo sapiens	Mutation(s): 0  Gene Names: TCL1A, TCL1
UniProt & NIH Common Fund Data Resources
Find proteins for P56279 (Homo sapiens) Explore P56279  Go to UniProtKB:  P56279
PHAROS:  P56279 GTEx:  ENSG00000100721

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth A], J [auth F], K [auth F], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	Coot	0.9.8.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Liu, Q.T., Li, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release