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- EMDB-65774: Cryo-EM structure of Aspergillus fumigatus ErdS dimer with tRNA(A... -

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Basic information

Entry
Database: EMDB / ID: EMD-65774
TitleCryo-EM structure of Aspergillus fumigatus ErdS dimer with tRNA(Asp) acceptor stem in an intermediate position toward the ATT active site
Map data
Sample
  • Complex: Cryo-EM structure of Aspergillus fumigatus ErdS dimer with tRNA(Asp) acceptor stem in an intermediate position toward the ATT active site
    • Protein or peptide: Aspartate--tRNA ligase, cytoplasmic
    • RNA: tRNA(Asp)
KeywordstRNA binding / sterol binding / aminoacyltransferase / dimer / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
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 (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (mold) / Aspergillus fumigatus (mold)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsMurayama H / Nishimura M / Kise Y / Itoh Y / Nureki O
Funding support Japan, 2 items
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 HB / Ji J / Kleiner RE / Nishimura M / Kise Y / Hou Y-M / Mathieu F / Becker HD / Itoh Y / Fischer F / Nureki O
History
DepositionAug 9, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65774.png

Downloads & links

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Map

FileDownload / File: emd_65774.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 210 pix.
= 232.4 Å		1.11 Å/pix.
x 210 pix.
= 232.4 Å		1.11 Å/pix.
x 210 pix.
= 232.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.10667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.072
Minimum - Maximum-0.1931515 - 0.49082133
Average (Standard dev.)-0.00042423533 (±0.015752735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 232.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65774_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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Half map: #2

Fileemd_65774_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65774_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of Aspergillus fumigatus ErdS dimer with tRNA(A...

EntireName: Cryo-EM structure of Aspergillus fumigatus ErdS dimer with tRNA(Asp) acceptor stem in an intermediate position toward the ATT active site
Components
  • Complex: Cryo-EM structure of Aspergillus fumigatus ErdS dimer with tRNA(Asp) acceptor stem in an intermediate position toward the ATT active site
    • Protein or peptide: Aspartate--tRNA ligase, cytoplasmic
    • RNA: tRNA(Asp)

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Supramolecule #1: Cryo-EM structure of Aspergillus fumigatus ErdS dimer with tRNA(A...

SupramoleculeName: Cryo-EM structure of Aspergillus fumigatus ErdS dimer with tRNA(Asp) acceptor stem in an intermediate position toward the ATT active site
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (mold)

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Macromolecule #1: Aspartate--tRNA ligase, cytoplasmic

MacromoleculeName: Aspartate--tRNA ligase, cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: aspartate-tRNA ligase
Source (natural)Organism: Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293) (mold)
Molecular weightTheoretical: 107.780023 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSIKRALSKI RPKADDDSSK SNLSNGSSPR RSIFSSFLRD RDYVSSSDDG SDDSGSGSLS RNQQKRLARE QRRKQRSRLS EEQQSDDSE RRHKEEIAQA AREETAEMKA RYGELPLLQS TSRPREPRIR LEDISSSSVG QEVFFTARLH IIRRMSARLV F LVFRQRLT ...String:
MSIKRALSKI RPKADDDSSK SNLSNGSSPR RSIFSSFLRD RDYVSSSDDG SDDSGSGSLS RNQQKRLARE QRRKQRSRLS EEQQSDDSE RRHKEEIAQA AREETAEMKA RYGELPLLQS TSRPREPRIR LEDISSSSVG QEVFFTARLH IIRRMSARLV F LVFRQRLT TFQGVLHEKP GAKSIAMVQW AEHLRLGSIV RVRGIVQTPQ VPVLGCSIHD VELDVEQIHL VVHREEPVPF SV YEAEIRT AEEDKVEGRR SHLPDRTRLN NRILDLRTPT SQSIFRLQSA LCNIFRSSLD EQGFIEIHTP KLQGSATESG ASV FQVNYF GRDAFLAEAP QLAKQMAIAA DFERVYEIGA VFRAEPAPTA AALTEYTGLD IEMAIEEHYH EMLDVLDAVI KNML KGVYG RYRREIEIVK HQFPSEDVVW LEETPIIRFS DGIKMLNESG WRDEDGNPLP EDDDLHTRDE IRLGELVKEK YGTDY YILD KFPVAARPFF AMPDPEDPRF TNSFDIFIRG QEIVSGGQRI HDPRMLEESM RRSGINPDTM EDYLEGFRWG APPHAG AGV GLERLLMLLL KLGNIRLASL FHRDPKSFPP KPPALLLRHP ESSTIEPPWQ REGRGSLAKD ESELQPLEHL IANYGDA TS TSWGDERFKI WRDMATGAAV SYVPSSNNYA VIPGNPLCDP SQYNRIITQF LQWMRRETKY KPIWLLCSPE VESILGDK L GWRSLSCIAE ERVDPSRNQA ASDGEIARKI RRAENEGIKI VEMKYGEMVP DDVREKIDAR IQDWLANRKG TQVHLSEIH PWRDSEHRWY FYAVDKSGTI CAFVALAMLS PHFGMQVKYS FDFPGSPNGV IEYIVTHAIQ TAARAGTKSL TFGAGATATL TPGHNLHGA KIKMLQHTYE TLAKQFHLVR KSEFRAKLGA HEEPLYIAYP PHGLGSRGIR AVLHFFED

UniProtKB: Aspartate--tRNA ligase, cytoplasmic

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Macromolecule #2: tRNA(Asp)

MacromoleculeName: tRNA(Asp) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Aspergillus fumigatus (mold)
Molecular weightTheoretical: 24.070229 KDa
SequenceString:
UCCUCGAUGG UCUAACGGUC AUGAUUUCCG CUUGUCACGC GGGAGACCAG GGUUCGACUC CCUGUCGGGG AGCCA

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54142
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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