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- PDB-9os7: Mycoplasma penetrans Methionyl tRNA Synthetase is an Asymmetric D... -

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Basic information

Entry
Database: PDB / ID: 9os7
TitleMycoplasma penetrans Methionyl tRNA Synthetase is an Asymmetric Dimer fused to N-terminal Ancillary Domains
Components(Methionine--tRNA ligase) x 2
KeywordsLIGASE / Methionine / tRNA transferase / Mycoplasma pentrans / graphene
Function / homology
Function and homology information


methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / ATP binding / cytoplasm
Similarity search - Function
Methionine-tRNA synthetase, type 2 / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminotransferase class V domain / Aminotransferase class-V / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site ...Methionine-tRNA synthetase, type 2 / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminotransferase class V domain / Aminotransferase class-V / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Rossmann-like alpha/beta/alpha sandwich fold / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Methionine--tRNA ligase
Similarity search - Component
Biological speciesMalacoplasma penetrans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsGhazi Esfahani, B. / Bowman, M. / Alexander, R. / Stroupe, M.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1856502 United States
National Science Foundation (NSF, United States)CHE1904612 United States
CitationJournal: To Be Published
Title: Mycoplasma penetrans Methionyl tRNA Synthetase is an Asymmetric Dimer fused to N-terminal Ancillary Domains
Authors: Ghazi Esfahani, B. / Bowman, M. / Alexander, R. / Stroupe, M.E.
History
DepositionMay 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine--tRNA ligase
B: Methionine--tRNA ligase
C: Methionine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)186,8243
Polymers186,8243
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Only one c-termini domain is resolved.
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 63656.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malacoplasma penetrans (bacteria) / Gene: metG, MYPE9380 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EUI8, methionine-tRNA ligase
#2: Protein Methionine--tRNA ligase / Methionyl-tRNA synthetase / MetRS


Mass: 59510.004 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 582-1087)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malacoplasma penetrans (bacteria) / Gene: metG, MYPE9380 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EUI8, methionine-tRNA ligase
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Mycoplasma penetrans methionyl tRNA synthetase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Malacoplasma penetrans (bacteria)
Source (recombinant)Organism: Ecoli xl10gold
Buffer solutionpH: 7.8
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON APOLLO (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.6particle selectionblob picker
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60101 / Symmetry type: POINT

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