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)

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZU0

This is version 1.0 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6U3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain C [auth A] MOL2 format, chain D [auth C] MOL2 format, chain C [auth A] mmCIF format, chain D [auth C] mmCIF format, chain C [auth A]	C [auth A], D [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.