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- PDB-8zu0: CryoEM structure of a tRNA uridine 5-carboxymethylaminomethyl mod... -

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Basic information

Entry
Database: PDB / ID: 8zu0
TitleCryoEM structure of a tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA
ComponentstRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
KeywordsHYDROLASE / Cellulose mutant
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 K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsJiang, W.X. / Cheng, X.Q. / Dong, X. / Ma, L.X. / Xing, Q.
Funding support China, 2items
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, W.X. / Cheng, X.Q. / Dong, X. / Ma, L.X. / Xing, Q.
History
DepositionJun 7, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 18, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jun 18, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)127,4844
Polymers125,9132
Non-polymers1,5712
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 62956.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mnmG, gidA, trmF, b3741, JW3719 / Production host: Escherichia coli BL21(DE3) (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 modificationY

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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: tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Acetivibrio thermocellus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77158 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 67.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0058918
ELECTRON MICROSCOPYf_angle_d0.56112086
ELECTRON MICROSCOPYf_chiral_restr0.04051330
ELECTRON MICROSCOPYf_plane_restr0.00411598
ELECTRON MICROSCOPYf_dihedral_angle_d4.35871224

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