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- EMDB-27871: CryoEM structure of yeast Arginyltransferase 1 (ATE1) -

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Basic information

Entry
Database: EMDB / ID: EMD-27871
TitleCryoEM structure of yeast Arginyltransferase 1 (ATE1)
Map data
Sample
  • Complex: apo form of yeast Arginyltransferase 1
    • Protein or peptide: Arginyl-tRNA--protein transferase 1
  • Ligand: ZINC ION
KeywordsArginyltransferase / post-translational modification / enzyme / TRANSFERASE
Function / homology
Function and homology information


arginyltransferase / arginyl-tRNA--protein transferase activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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
DepositionAug 17, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27871.png

Downloads & links

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Map

FileDownload / File: emd_27871.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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: 0.1
Minimum - Maximum-0.34355107 - 0.51378316
Average (Standard dev.)0.000011341188 (±0.010643962)
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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Half map: #2

Fileemd_27871_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27871_half_map_2.map
Projections & Slices
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Sample components

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Entire : apo form of yeast Arginyltransferase 1

EntireName: apo form of yeast Arginyltransferase 1
Components
  • Complex: apo form of yeast Arginyltransferase 1
    • Protein or peptide: Arginyl-tRNA--protein transferase 1
  • Ligand: ZINC ION

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Supramolecule #1: apo form of yeast Arginyltransferase 1

SupramoleculeName: apo form of yeast Arginyltransferase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 58.001277 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / 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

Startup modelType of model: INSILICO MODEL / Details: AlphaFold II predicted model AF-P16639-F1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 523915
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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