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- PDB-8tzv: Apo form of human ATE1 -

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Basic information

Entry
Database: PDB / ID: 8tzv
TitleApo form of human ATE1
ComponentsIsoform ATE1-2 of Arginyl-tRNA--protein transferase 1
KeywordsTRANSFERASE / arginylation / ATE1 / apo
Function / homology
Function and homology information


protein arginylation / arginyltransferase / arginyl-tRNA--protein transferase activity / proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / response to oxidative stress / nucleus / cytoplasm
Similarity search - Function
Arginine-tRNA-protein transferase 1, eukaryotic / 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 speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHuang, W. / Zhang, Y. / Taylor, D.J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA241301 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA240993 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM133841 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142002 United States
CitationJournal: Nat Commun / Year: 2024
Title: Oligomerization and a distinct tRNA-binding loop are important regulators of human arginyl-transferase function.
Authors: Xin Lan / Wei Huang / Su Bin Kim / Dechen Fu / Thilini Abeywansha / Jiemin Lou / Udayakumaran Balamurugan / Yong Tae Kwon / Chang Hoon Ji / Derek J Taylor / Yi Zhang /
Abstract: The arginyl-transferase ATE1 is a tRNA-dependent enzyme that covalently attaches an arginine molecule to a protein substrate. Conserved from yeast to humans, ATE1 deficiency in mice correlates with ...The arginyl-transferase ATE1 is a tRNA-dependent enzyme that covalently attaches an arginine molecule to a protein substrate. Conserved from yeast to humans, ATE1 deficiency in mice correlates with defects in cardiovascular development and angiogenesis and results in embryonic lethality, while conditional knockouts exhibit reproductive, developmental, and neurological deficiencies. Despite the recent revelation of the tRNA binding mechanism and the catalytic cycle of yeast ATE1, the structure-function relationship of ATE1 in higher organisms is not well understood. In this study, we present the three-dimensional structure of human ATE1 in an apo-state and in complex with its tRNA cofactor and a peptide substrate. In contrast to its yeast counterpart, human ATE1 forms a symmetric homodimer, which dissociates upon binding of a substrate. Furthermore, human ATE1 includes a unique and extended loop that wraps around tRNA, creating extensive contacts with the T-arm of the tRNA cofactor. Substituting key residues identified in the substrate binding site of ATE1 abolishes enzymatic activity and results in the accumulation of ATE1 substrates in cells.
History
DepositionAug 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1
B: Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3974
Polymers118,2662
Non-polymers1312
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 Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1


Mass: 59132.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATE1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O95260
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: Arginyl-tRNA--protein transferase 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
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: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 34 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228665 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0015848
ELECTRON MICROSCOPYf_angle_d0.3747906
ELECTRON MICROSCOPYf_dihedral_angle_d7.7722212
ELECTRON MICROSCOPYf_chiral_restr0.039802
ELECTRON MICROSCOPYf_plane_restr0.0031024

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