7F4T | pdb_00007f4t

Crystal structure of SAM-bound TthMTA1-Ptep2 complex

• PDB DOI: https://doi.org/10.2210/pdb7F4T/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Tetrahymena thermophila SB210, Paramecium tetraurelia strain d4-2
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2021-06-21 Released: 2022-06-15 
• Deposition Author(s): Chen, J., Liu, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.68 Å
• R-Value Free: 
  0.329 (Depositor), 0.329 (DCC) 
• R-Value Work: 
  0.283 (Depositor), 0.283 (DCC) 
• R-Value Observed: 
  0.286 (Depositor) 

Starting Model: experimental

Literature

Structural basis for MTA1c-mediated DNA N6-adenine methylation

Chen, J., Hu, R., Chen, Y., Lin, X., Xiang, W., Chen, H., Yao, C., Liu, L.

(2022) Nat Commun 13: 3257

• DOI: https://doi.org/10.1038/s41467-022-31060-6

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 175.91 kDa 
• Atom Count: 10,725 
• Modeled Residue Count: 1,370 
• Deposited Residue Count: 1,500 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MT-a70 family protein	A, B [auth E], C [auth H], D [auth K]	247	Tetrahymena thermophila SB210	Mutation(s): 0  Gene Names: MTA1 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
Ptep2	E [auth B], F [auth D], G, H [auth J]	128	Paramecium tetraurelia strain d4-2	Mutation(s): 0
UniProt
Find proteins for A0DWP1 (Paramecium tetraurelia) Explore A0DWP1  Go to UniProtKB:  A0DWP1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.68 Å
• R-Value Free:  0.329 (Depositor), 0.329 (DCC) 
• R-Value Work:  0.283 (Depositor), 0.283 (DCC) 
• R-Value Observed: 0.286 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.13	α = 90
b = 110.193	β = 91.642
c = 102.636	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-15 
Deposition Author(s): Chen, J., Liu, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32022047

Revision History  

• Version 1.0: 2022-06-15
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description