7F4P | pdb_00007f4p

Crystal structure of SAM-bound MTA1-p2 complex

PDB DOI: https://doi.org/10.2210/pdb7F4P/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free:
0.265 (Depositor), 0.262 (DCC)
R-Value Work:
0.249 (Depositor), 0.247 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 45.49 kDa
Atom Count: 2,821
Modeled Residue Count: 347
Deposited Residue Count: 389
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein, putative	A [auth B]	142	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I7M8B9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MT-a70 family protein	B [auth A]	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q22GC0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.98 Å
R-Value Free: 0.265 (Depositor), 0.262 (DCC)
R-Value Work: 0.249 (Depositor), 0.247 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.032	α = 90
b = 137.032	β = 90
c = 61.629	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-15

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.