+Open data
-Basic information
Entry | Database: PDB / ID: 8tzv | |||||||||||||||
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Title | Apo form of human ATE1 | |||||||||||||||
Components | Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1 | |||||||||||||||
Keywords | TRANSFERASE / 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 | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
Authors | Huang, W. / Zhang, Y. / Taylor, D.J. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8tzv.cif.gz | 154.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8tzv.ent.gz | 118 KB | Display | PDB format |
PDBx/mmJSON format | 8tzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tzv_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8tzv_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8tzv_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 8tzv_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/8tzv ftp://data.pdbj.org/pub/pdb/validation_reports/tz/8tzv | HTTPS FTP |
-Related structure data
Related structure data | 41770MC 8uauC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Arginyl-tRNA--protein transferase 1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 34 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228665 / Symmetry type: POINT | ||||||||||||||||||||||||
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