7F4M

Crystal structure of SAM-bound MTA1-p1-p2 complex

• PDB DOI: https://doi.org/10.2210/pdb7F4M/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Tetrahymena thermophila SB210
• 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: 3.58 Å
• R-Value Free: 0.276 
• R-Value Work: 0.251 
• R-Value Observed: 0.252 

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 3-mer - A1B1C1 

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 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 162.09 kDa 
• Atom Count: 6,193 
• Modelled Residue Count: 752 
• Deposited Residue Count: 1,396 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein, putative	A [auth B], F [auth A]	142	Tetrahymena thermophila SB210	Mutation(s): 0  Gene Names: p2
UniProt
Find proteins for I7M8B9 (Tetrahymena thermophila (strain SB210)) Explore I7M8B9  Go to UniProtKB:  I7M8B9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MT-a70 family protein	B [auth C], C [auth D]	247	Tetrahymena thermophila SB210	Mutation(s): 0  Gene Names: MTA1
UniProt
Find proteins for Q22GC0 (Tetrahymena thermophila (strain SB210)) Explore Q22GC0  Go to UniProtKB:  Q22GC0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
p1 protein	D [auth E], E [auth F]	309	Tetrahymena thermophila SB210	Mutation(s): 0
UniProt
Find proteins for Q22VV9 (Tetrahymena thermophila (strain SB210)) Explore Q22VV9  Go to UniProtKB:  Q22VV9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free: 0.276 
• R-Value Work: 0.251 
• R-Value Observed: 0.252 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.517	α = 90
b = 85.786	β = 90
c = 162.903	γ = 90

Software Package:

Software Name	Purpose
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