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- PDB-9hir: MnmG dimer within the MnmE-MnmG a4b2 complex -

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Basic information

Entry
Database: PDB / ID: 9hir
TitleMnmG dimer within the MnmE-MnmG a4b2 complex
ComponentstRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
KeywordsRNA BINDING PROTEIN / tRNA modification / FAD binding protein
Function / homology
Function and homology information


regulation of cytoplasmic translational fidelity / cytosolic tRNA wobble base thiouridylase complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / tRNA methylation / response to UV / flavin adenine dinucleotide binding / protein homodimerization activity / cytosol
Similarity search - Function
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal / tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain / : / : / tRNA modifying enzyme MnmG/GidA C-terminal helical bundle / tRNA modifying enzyme MnmG/GidA C-terminal helical domain / Glucose inhibited division protein A family signature 1. / GidA associated domain 3 / MnmG-related, conserved site ...tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal / tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain / : / : / tRNA modifying enzyme MnmG/GidA C-terminal helical bundle / tRNA modifying enzyme MnmG/GidA C-terminal helical domain / Glucose inhibited division protein A family signature 1. / GidA associated domain 3 / MnmG-related, conserved site / Glucose inhibited division protein A family signature 2. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related / MnmG, N-terminal domain / Glucose inhibited division protein A / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.12 Å
AuthorsMaes, L. / Galicia, C. / Fislage, M. / Versees, W.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Vrije Universiteit BrusselSRP95 Belgium
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Cryo-EM structures of the MnmE-MnmG complex reveal large conformational changes and provide new insights into the mechanism of tRNA modification
Authors: Maes, L. / Mares-Mejia, I. / Martin, E. / Bickel, D. / Claeys, S. / Vranken, W. / Fislage, M. / Galicia, C. / Versees, W.
History
DepositionNov 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
D: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,3264
Polymers143,7552
Non-polymers1,5712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / Glucose-inhibited division protein A


Mass: 71877.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MnmG bound to FAD / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mnmG, gidA, trmF, b3741, JW3719 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A6U3
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MnmE-MnmG complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.55 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 62 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2SerialEM3.0.8image acquisition
9PHENIX1.21model refinement
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107190 / Details: Local refinement map / Symmetry type: POINT
RefinementHighest resolution: 4.12 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039963
ELECTRON MICROSCOPYf_angle_d0.64413510
ELECTRON MICROSCOPYf_dihedral_angle_d6.2031462
ELECTRON MICROSCOPYf_chiral_restr0.0431498
ELECTRON MICROSCOPYf_plane_restr0.0041779

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