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- PDB-9w9e: Cryo-EM structure of Aspergillus fumigatus ErdS tetramer -

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Basic information

Entry
Database: PDB / ID: 9w9e
TitleCryo-EM structure of Aspergillus fumigatus ErdS tetramer
ComponentsAspartate--tRNA ligase, cytoplasmic
KeywordsRNA BINDING PROTEIN / tRNA binding / sterol binding / aminoacyltransferase / tetramer
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartate-tRNA ligase activity / aspartyl-tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / RNA binding / ATP binding / cytosol
Similarity search - Function
Aspartate-tRNA synthetase, type 2 / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Aspartate--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMurayama, H. / Nishimura, M. / Kise, Y. / Itoh, Y. / Nureki, O.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR20E2 Japan
Japan Society for the Promotion of Science (JSPS)23KJ0722 Japan
CitationJournal: To Be Published
Title: Structural basis for tRNA-dependent sterol aminoacylation underlying cell membrane integrity
Authors: Murayama, H. / Yakobov, N. / Mahmoudi, N. / Sasha, L. / Zuttion, S. / Senger, B. / Huck, L. / Gamper, H.B. / Ji, J. / Kleiner, R.E. / Nishimura, M. / Kise, Y. / Hou, Y.-M. / Mathieu, F. / ...Authors: Murayama, H. / Yakobov, N. / Mahmoudi, N. / Sasha, L. / Zuttion, S. / Senger, B. / Huck, L. / Gamper, H.B. / Ji, J. / Kleiner, R.E. / Nishimura, M. / Kise, Y. / Hou, Y.-M. / Mathieu, F. / Becker, H.D. / Itoh, Y. / Fischer, F. / Nureki, O.
History
DepositionAug 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 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

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Assembly

Deposited unit
A: Aspartate--tRNA ligase, cytoplasmic
B: Aspartate--tRNA ligase, cytoplasmic
C: Aspartate--tRNA ligase, cytoplasmic
D: Aspartate--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)393,8834
Polymers393,8834
Non-polymers00
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
Aspartate--tRNA ligase, cytoplasmic / Aspartyl-tRNA synthetase


Mass: 98470.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_1G02570 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WKG3, aspartate-tRNA ligase
Has protein modificationN

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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: Cryo-EM structure of Aspergillus fumigatus ErdS tetramer
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (mold)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 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: 1600 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35812 / Symmetry type: POINT

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