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- EMDB-42071: human ATE1 in complex with Arg-tRNA and a peptide substrate -

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Basic information

Entry
Database: EMDB / ID: EMD-42071
Titlehuman ATE1 in complex with Arg-tRNA and a peptide substrate
Map data
Sample
  • Complex: Arginyl-tRNA--protein transferase 1/RNA complex
    • Protein or peptide: Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1
    • Protein or peptide: substrate
    • RNA: RNA (76-MER)
  • Ligand: ZINC ION
Keywordsarginylation / ATE1 / complex / TRANSFERASE-RNA complex
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsHuang W / Zhang Y / Taylor DJ
Funding support United States, 4 items
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
DepositionSep 22, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42071.png

Downloads & links

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Map

FileDownload / File: emd_42071.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.05 Å/pix.
x 60 pix.
= 423. Å		7.05 Å/pix.
x 60 pix.
= 423. Å		7.05 Å/pix.
x 60 pix.
= 423. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.2.082.082.08
CCP4 map header7.057.057.05
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.23708396 - 0.5367093
Average (Standard dev.)-0.0014551308 (±0.023725603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 208.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Arginyl-tRNA--protein transferase 1/RNA complex

EntireName: Arginyl-tRNA--protein transferase 1/RNA complex
Components
  • Complex: Arginyl-tRNA--protein transferase 1/RNA complex
    • Protein or peptide: Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1
    • Protein or peptide: substrate
    • RNA: RNA (76-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Arginyl-tRNA--protein transferase 1/RNA complex

SupramoleculeName: Arginyl-tRNA--protein transferase 1/RNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1

MacromoleculeName: Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.132898 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: GPAFWAGGSP SVVDYFPSED FYRCGYCKNE SGSRSNGMWA HSMTVQDYQD LIDRGWRRSG KYVYKPVMNQ TCCPQYTIRC RPLQFQPSK SHKKVLKKML KFLAKGEVPK GSCEDEPMDS TMDDAVAGDF ALINKLDIQC DLKTLSDDIK ESLESEGKNS K KEEPQELL ...String:
GPAFWAGGSP SVVDYFPSED FYRCGYCKNE SGSRSNGMWA HSMTVQDYQD LIDRGWRRSG KYVYKPVMNQ TCCPQYTIRC RPLQFQPSK SHKKVLKKML KFLAKGEVPK GSCEDEPMDS TMDDAVAGDF ALINKLDIQC DLKTLSDDIK ESLESEGKNS K KEEPQELL QSQDFVGEKL GSGEPSHSVK VHTVPKPGKG ADLSKPPCRK AKEIRKERKR LKLMQQNPAG ELEGFQAQGH PP SLFPPKA KSNQPKSLED LIFESLPENA SHKLEVRLVP VSFEDPEFKS SFSQSFSLYV KYQVAIHQDP PDECGKTEFT RFL CSSPLE AETPPNGPDC GYGSFHQQYW LDGKIIAVGV IDILPNCVSS VYLYYDPDYS FLSLGVYSAL REIAFTRQLH EKTS QLSYY YMGFYIHSCP KMKYKGQYRP SDLLCPETYV WVPIEQCLPS LENSKYCRFN QDPEAVDEDR STEPDRLQVF HKRAI MPYG VYKKQQKDPS EEAAVLQYAS LVGQKCSERM LLFRN

UniProtKB: Arginyl-tRNA--protein transferase 1

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Macromolecule #2: substrate

MacromoleculeName: substrate / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.188244 KDa
SequenceString:
DDIAALVVDN GS

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Macromolecule #3: RNA (76-MER)

MacromoleculeName: RNA (76-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.456488 KDa
SequenceString:
GGCUCUGUGG CGCAAUGGAU AGCGCAUUGG ACUUCUAAUU CAAAGGUUGU GGGUUCGAAU CCCACCAGAG UCGCCA

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 219685
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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