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- EMDB-52197: MnmE-MnmG a2b2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-52197
TitleMnmE-MnmG a2b2 complex
Map data
Sample
  • Complex: MnmE-MnmG complex
    • Protein or peptide: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
  • Protein or peptide: tRNA modification GTPase MnmE
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordstRNA modification / FAD binding protein / folate binding protein / G protein activated by dimerization / 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 / Hydrolases; Acting on acid anhydrides / tRNA wobble uridine modification / tRNA methylation / response to pH / potassium ion binding / response to UV / : ...regulation of cytoplasmic translational fidelity / cytosolic tRNA wobble base thiouridylase complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / Hydrolases; Acting on acid anhydrides / tRNA wobble uridine modification / tRNA methylation / response to pH / potassium ion binding / response to UV / : / GDP binding / flavin adenine dinucleotide binding / GTPase activity / GTP binding / protein homodimerization activity / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal ...tRNA modification GTPase MnmE / GTP-binding protein TrmE, N-terminal / MnmE, helical domain / tRNA modification GTPase MnmE domain 2 / TrmE-type guanine nucleotide-binding domain / GTP-binding protein TrmE N-terminus / MnmE helical domain / TrmE-type guanine nucleotide-binding (G) domain profile. / 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 / GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1 / 50S ribosome-binding GTPase / GTP binding domain / FAD/NAD(P)-binding domain superfamily / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA modification GTPase MnmE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 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_52197.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.7596 Å
Density
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-53.268203999999997 - 77.264859999999999
Average (Standard dev.)0.000000000000038 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 388.9152 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
  • Protein or peptide: tRNA modification GTPase MnmE
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • 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: #2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: tRNA modification GTPase MnmE

MacromoleculeName: tRNA modification GTPase MnmE / type: protein_or_peptide / ID: 1 / Details: MnmE bound to GTP analogue / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 49.286699 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP FKDADGSVLD QGIALWFPGP NSFTGEDVLE LQGHGGPVI LDLLLKRILT IPGLRIARPG EFSERAFLND KLDLAQAEAI ADLIDASSEQ AARSALNSLQ GAFSARVNHL V EALTHLRI ...String:
MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP FKDADGSVLD QGIALWFPGP NSFTGEDVLE LQGHGGPVI LDLLLKRILT IPGLRIARPG EFSERAFLND KLDLAQAEAI ADLIDASSEQ AARSALNSLQ GAFSARVNHL V EALTHLRI YVEAAIDFPD EEIDFLSDGK IEAQLNDVIA DLDAVRAEAR QGSLLREGMK VVIAGRPNAG KSSLLNALAG RE AAIVTDI AGTTRDVLRE HIHIDGMPLH IIDTAGLREA SDEVERIGIE RAWQEIEQAD RVLFMVDGTT TDAVDPAEIW PEF IARLPA KLPITVVRNK ADITGETLGM SEVNGHALIR LSARTGEGVD VLRNHLKQSM GFDTNMEGGF LARRRHLQAL EQAA EHLQQ GKAQLLGAWA GELLAEELRL AQQNLSEITG EFTSDDLLGR IFSSFCIGK

UniProtKB: tRNA modification GTPase MnmE

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Macromolecule #2: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG

MacromoleculeName: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
type: protein_or_peptide / ID: 2 / 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 #3: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec.
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: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 116023
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9hip:
MnmE-MnmG a2b2 complex

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