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- EMDB-29638: CryoEM structure of yeast Arginyltransferase 1 (ATE1) -

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Basic information

Entry
Database: EMDB / ID: EMD-29638
TitleCryoEM structure of yeast Arginyltransferase 1 (ATE1)
Map data
Sample
  • Complex: yeast Arginyltransferase 1 bound to Arg tRNA
    • Protein or peptide: Arginyl-tRNA--protein transferase 1
    • RNA: Arg tRNA
  • Ligand: ZINC ION
KeywordsArginyltransferase / post-translational modification / enzyme / TRANSFERASE-RNA complex
Function / homology
Function and homology information


arginyltransferase / arginyl-tRNA--protein transferase activity / proteasomal protein catabolic process / cytoplasm
Similarity search - Function
N-end aminoacyl transferase, N-terminal / N-end rule aminoacyl transferase, C-terminal / N-end rule aminoacyl transferase / Arginine-tRNA-protein transferase, N terminus / Arginine-tRNA-protein transferase, C terminus / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Arginyl-tRNA--protein transferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHuang W / Zhang Y / Taylor DJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133841 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA241301 United States
CitationJournal: Nat Commun / Year: 2023
Title: The structural basis of tRNA recognition by arginyl-tRNA-protein transferase.
Authors: Thilini Abeywansha / Wei Huang / Xuan Ye / Allison Nawrocki / Xin Lan / Eckhard Jankowsky / Derek J Taylor / Yi Zhang /
Abstract: Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its ...Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto its protein substrates in a tRNA-dependent manner. However, how ATE1 (and other aminoacyl-tRNA transferases) hijacks tRNA from the highly efficient ribosomal protein synthesis pathways and catalyzes the arginylation reaction remains a mystery. Here, we describe the three-dimensional structures of Saccharomyces cerevisiae ATE1 with and without its tRNA cofactor. Importantly, the putative substrate binding domain of ATE1 adopts a previously uncharacterized fold that contains an atypical zinc-binding site critical for ATE1 stability and function. The unique recognition of tRNA by ATE1 is coordinated through interactions with the major groove of the acceptor arm of tRNA. Binding of tRNA induces conformational changes in ATE1 that helps explain the mechanism of substrate arginylation.
History
DepositionJan 29, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29638.png

Downloads & links

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Map

FileDownload / File: emd_29638.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 256 pix.
= 223.386 Å		0.87 Å/pix.
x 256 pix.
= 223.386 Å		0.87 Å/pix.
x 256 pix.
= 223.386 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.009751085 - 0.017039202
Average (Standard dev.)0.000039301063 (±0.00043084196)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 223.3856 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Phenix auto-sharpen map

Fileemd_29638_additional_1.map
AnnotationPhenix auto-sharpen map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_29638_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_29638_half_map_2.map
Projections & Slices
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Sample components

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Entire : yeast Arginyltransferase 1 bound to Arg tRNA

EntireName: yeast Arginyltransferase 1 bound to Arg tRNA
Components
  • Complex: yeast Arginyltransferase 1 bound to Arg tRNA
    • Protein or peptide: Arginyl-tRNA--protein transferase 1
    • RNA: Arg tRNA
  • Ligand: ZINC ION

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Supramolecule #1: yeast Arginyltransferase 1 bound to Arg tRNA

SupramoleculeName: yeast Arginyltransferase 1 bound to Arg tRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Arginyl-tRNA--protein transferase 1

MacromoleculeName: Arginyl-tRNA--protein transferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: arginyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 58.001277 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSDRFVIWAP SMHNEPAAKC GYCHGNKGGN MDQLFALDSW AHRYMNKMDV VKIENCTIGS FVEHMDVATY DRMCNMGFRR SGKFLYKVD PLRNCCRLYT IRTAPQELNM TKELKKCISR FATRITSEDY CPAAVASSDF VGKIVNAEMN SKTFYTRFEP A LYSEEKYH ...String:
MSDRFVIWAP SMHNEPAAKC GYCHGNKGGN MDQLFALDSW AHRYMNKMDV VKIENCTIGS FVEHMDVATY DRMCNMGFRR SGKFLYKVD PLRNCCRLYT IRTAPQELNM TKELKKCISR FATRITSEDY CPAAVASSDF VGKIVNAEMN SKTFYTRFEP A LYSEEKYH LFVKYQEKVH QDYNNSPKSF KRFLCDTPFG PEAVLGTQES WEQLNNWQRM KPGEKLKHMG PVHECYYYEG KL IAITVSD ILPSGISSVY FIWDPDYSKW SLGKLSALRD LAIIQRTNLQ YYYLGYYIED CPKMNYKANY GAEVLDVCHS KYI PLKPIQ DMISRGKLFV IGEEETKVTK ELYLVDSETG RGEGFPTDNV VKYKNIAEEI YGVGGCAFKS ANESALELKE LYGI PYEEE DLDTIYHLKE HNGHAPNGIP NVVPGLLPLW ELLDIMQSGK ITDLEGRLFL FEIETEGIRP LINFYSEPPN VKKRI CDVI RLFGFETCMK AVILYSEQM

UniProtKB: Arginyl-tRNA--protein transferase 1

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Macromolecule #2: Arg tRNA

MacromoleculeName: Arg tRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.789736 KDa
SequenceString:
GCGCCCUUAG CUCAGUUGGA UAGAGCAACG ACCUUCUAAG UCGUGGGCCG CAGGUUCGAA UCCUGCAGGG CGCGCCA

GENBANK: GENBANK: CP026935.2

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.1
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 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: INSILICO MODEL / Details: AlphaFold II predicted mode AF-P16639-F1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 208051
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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