8XYX | pdb_00008xyx

Cryo-EM structure of SAM-bound Tetrahymena DNA methyltransferase complex MTA1c (D209A)

• PDB DOI: https://doi.org/10.2210/pdb8XYX/pdb
• EM Map EMD-38782: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Tetrahymena thermophila SB210
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-01-20 Released: 2025-07-23 
• Deposition Author(s): Xu, Q., Shi, Z.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Structures of Tetrahymena DNA methyltransferase MTA1c

Xu, Q., Xie, Y., Shi, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 143.97 kDa 
• Atom Count: 5,292 
• Modeled Residue Count: 641 
• Deposited Residue Count: 1,245 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MT-a70 family protein	A	378	Tetrahymena thermophila SB210	Mutation(s): 1  Gene Names: TTHERM_00704040 EC: 2.1.1.348
UniProt
Find proteins for Q22GC0 (Tetrahymena thermophila (strain SB210)) Explore Q22GC0  Go to UniProtKB:  Q22GC0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methyltransferase MT, putative	B	357	Tetrahymena thermophila SB210	Mutation(s): 0  Gene Names: TTHERM_01005150
UniProt
Find proteins for Q22XT1 (Tetrahymena thermophila (strain SB210)) Explore Q22XT1  Go to UniProtKB:  Q22XT1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Myb-like DNA-binding domain protein	C	364	Tetrahymena thermophila SB210	Mutation(s): 0  Gene Names: TTHERM_00161750
UniProt
Find proteins for Q22VV9 (Tetrahymena thermophila (strain SB210)) Explore Q22VV9  Go to UniProtKB:  Q22VV9

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein, putative	D	146	Tetrahymena thermophila SB210	Mutation(s): 0  Gene Names: TTHERM_00439330
UniProt
Find proteins for I7M8B9 (Tetrahymena thermophila (strain SB210)) Explore I7M8B9  Go to UniProtKB:  I7M8B9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	E [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Xu, Q., Shi, Z.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271264

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release