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- EMDB-52199: Focused map of the MnmG dimer within the MnmE-MnmG a4b2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-52199
TitleFocused map of the MnmG dimer within the MnmE-MnmG a4b2 complex
Map data
Sample
  • Complex: MnmE-MnmG complex
    • Protein or peptide: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordstRNA modification / FAD binding protein / RNA 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
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.12 Å
AuthorsMaes L / Galicia C / Fislage M / Versees W
Funding support Belgium, 1 items
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, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_52199.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.5192 Å
Density
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-6.42009 - 10.221622
Average (Standard dev.)0.000000000022843 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin125146135
Dimensions876367
Spacing678763
CellA: 101.7864 Å / B: 132.1704 Å / C: 95.709595 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : MnmE-MnmG complex

EntireName: MnmE-MnmG complex
Components
  • Complex: MnmE-MnmG complex
    • Protein or peptide: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE

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Supramolecule #1: MnmE-MnmG complex

SupramoleculeName: MnmE-MnmG complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG

MacromoleculeName: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
type: protein_or_peptide / ID: 1 / Details: MnmG bound to FAD / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 71.8775 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SSGENLYFQG MFYPDPFDVI IIGGGHAGTE AAMAAARMGQ QTLLLTHNID TLGQMSCNPA IGGIGKGHLV KEVDALGGL MAKAIDQAGI QFRILNASKG PAVRATRAQA DRVLYRQAVR TALENQPNLM IFQQAVEDLI VENDRVVGAV T QMGLKFRA ...String:
MGSSHHHHHH SSGENLYFQG MFYPDPFDVI IIGGGHAGTE AAMAAARMGQ QTLLLTHNID TLGQMSCNPA IGGIGKGHLV KEVDALGGL MAKAIDQAGI QFRILNASKG PAVRATRAQA DRVLYRQAVR TALENQPNLM IFQQAVEDLI VENDRVVGAV T QMGLKFRA KAVVLTVGTF LDGKIHIGLD NYSGGRAGDP PSIPLSRRLR ELPLRVGRLK TGTPPRIDAR TIDFSVLAQQ HG DNPMPVF SFMGNASQHP QQVPCYITHT NEKTHDVIRS NLDRSPMYAG VIEGVGPRYC PSIEDKVMRF ADRNQHQIFL EPE GLTSNE IYPNGISTSL PFDVQMQIVR SMQGMENAKI VRPGYAIEYD FFDPRDLKPT LESKFIQGLF FAGQINGTTG YEEA AAQGL LAGLNAARLS ADKEGWAPAR SQAYLGVLVD DLCTLGTKEP YRMFTSRAEY RLMLREDNAD LRLTEIGREL GLVDD ERWA RFNEKLENIE RERQRLKSTW VTPSAEAAAE VNAHLTAPLS REASGEDLLR RPEMTYEKLT TLTPFAPALT DEQAAE QVE IQVKYEGYIA RQQDEIEKQL RNENTLLPAT LDYRQVSGLS NEVIAKLNDH KPASIGQASR ISGVTPAAIS ILLVWLK KQ GMLRRSA

UniProtKB: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG

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Macromolecule #2: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.55 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Details: Local refinement map / Number images used: 107190
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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