8ZU0 | pdb_00008zu0

CryoEM structure of a tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA

• PDB DOI: https://doi.org/10.2210/pdb8ZU0/pdb
• EM Map EMD-60477: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-07 Released: 2025-06-18 
• Deposition Author(s): Jiang, W.X., Cheng, X.Q., Dong, X., Ma, L.X., Xing, Q.
• Funding Organization(s): National Basic Research Program of China (973 Program), National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

CryoEM structure of a tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA

Jiang, W.X., Cheng, X.Q., Dong, X., Ma, L.X., Xing, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 127.48 kDa 
• Atom Count: 8,752 
• Modeled Residue Count: 1,108 
• Deposited Residue Count: 1,134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG	A, B [auth C]	567	Escherichia coli K-12	Mutation(s): 0  Gene Names: mnmG, gidA, trmF, b3741, JW3719
UniProt
Find proteins for P0A6U3 (Escherichia coli (strain K12)) Explore P0A6U3  Go to UniProtKB:  P0A6U3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	C [auth A], D [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Jiang, W.X., Cheng, X.Q., Dong, X., Ma, L.X., Xing, Q.

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Funding Organization	Location	Grant Number
National Basic Research Program of China (973 Program)	China	2021YFC2100100
National Science Foundation (NSF, China)	China	32371277

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release