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- EMDB-60477: CryoEM structure of a tRNA uridine 5-carboxymethylaminomethyl mod... -

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Basic information

Entry
Database: EMDB / ID: EMD-60477
TitleCryoEM structure of a tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA
Map data
Sample
  • Complex: tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA
    • Protein or peptide: tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
KeywordsCellulose mutant / HYDROLASE
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 speciesAcetivibrio thermocellus (bacteria) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsJiang WX / Cheng XQ / Dong X / Ma LX / Xing Q
Funding support China, 2 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFC2100100 China
National Science Foundation (NSF, China)32371277 China
CitationJournal: To Be Published
Title: CryoEM structure of a tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA
Authors: Jiang WX / Cheng XQ / Dong X / Ma LX / Xing Q
History
DepositionJun 7, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60477.png

Downloads & links

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Map

FileDownload / File: emd_60477.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.43 Å/pix.
x 480 pix.
= 204. Å		0.43 Å/pix.
x 480 pix.
= 204. Å		0.43 Å/pix.
x 480 pix.
= 204. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.425 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0187
Minimum - Maximum-0.19489616 - 0.30751726
Average (Standard dev.)-0.00012455965 (±0.008226636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 204.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60477_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60477_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA

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

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Supramolecule #1: tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA

SupramoleculeName: tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acetivibrio thermocellus (bacteria)

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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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 62.956289 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MFYPDPFDVI IIGGGHAGTE AAMAAARMGQ QTLLLTHNID TLGQMSCNPA IGGIGKGHLV KEVDALGGLM AKAIDQAGIQ FRILNASKG PAVRATRAQA DRVLYRQAVR TALENQPNLM IFQQAVEDLI VENDRVVGAV TQMGLKFRAK AVVLTVGTFL D GKIHIGLD ...String:
MFYPDPFDVI IIGGGHAGTE AAMAAARMGQ QTLLLTHNID TLGQMSCNPA IGGIGKGHLV KEVDALGGLM AKAIDQAGIQ FRILNASKG PAVRATRAQA DRVLYRQAVR TALENQPNLM IFQQAVEDLI VENDRVVGAV TQMGLKFRAK AVVLTVGTFL D GKIHIGLD NYSGGRAGDP PSIPLSRRLR ELPLRVGRLK TGTPPRIDAR TIDFSVLAQQ HGDNPMPVFS FMGNASQHPQ QV PCYITHT NEKTHDVIRS NLDRSPMYAG VIEGVGPRYC PSIEDKVMRF ADRNQHQIFL EPEGLTSNEI YPNGISTSLP FDV QMQIVR SMQGMENAKI VRPGYAIEYD FFDPRDLKPT LESKFIQGLF FAGQINGTTG YEEAAAQGLL AGLNAARLSA DKEG WAPAR SQAYLGVLVD DLCTLGTKEP YRMFTSRAEY RLMLREDNAD LRLTEIGREL GLVDDERWAR FNEKLENIER ERQRL KSTW VTPSAEAAAE VNAHLTAPLS REASGEDLLR RPEMTYEKLT TLTPFAPALT DEQAAEQVEI QVKYEGYIAR QQDEIE KQL RNEN

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

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77158
Initial angle assignmentType: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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