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- PDB-8fzr: CryoEM structure of yeast Arginyltransferase 1 (ATE1) -

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Basic information

Entry
Database: PDB / ID: 8fzr
TitleCryoEM structure of yeast Arginyltransferase 1 (ATE1)
Components
  • Arg tRNA
  • Arginyl-tRNA--protein transferase 1
KeywordsTRANSFERASE/RNA / Arginyltransferase / 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
: / RNA / RNA (> 10) / Arginyl-tRNA--protein transferase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHuang, W. / Zhang, Y. / Taylor, D.J.
Funding support United States, 2items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginyl-tRNA--protein transferase 1
R: Arg tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8563
Polymers82,7912
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Arginyl-tRNA--protein transferase 1 / Arginyltransferase 1 / R-transferase 1 / Arginine-tRNA--protein transferase 1


Mass: 58001.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATE1, YGL017W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P16639, arginyltransferase
#2: RNA chain Arg tRNA


Mass: 24789.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: GenBank: 1845826323
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
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: yeast Arginyltransferase 1 bound to Arg tRNA / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.1
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 25000 nm / Nominal defocus min: 5000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208051 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 0 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00156006
ELECTRON MICROSCOPYf_angle_d0.41098497
ELECTRON MICROSCOPYf_chiral_restr0.0334977
ELECTRON MICROSCOPYf_plane_restr0.0034803
ELECTRON MICROSCOPYf_dihedral_angle_d15.4152487

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