+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41770 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Apo form of human ATE1 | |||||||||||||||
Map data | ||||||||||||||||
Sample |
| |||||||||||||||
Keywords | arginylation / ATE1 / apo / TRANSFERASE | |||||||||||||||
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 | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
Authors | Huang W / Zhang Y / Taylor DJ | |||||||||||||||
Funding support | United States, 4 items
| |||||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_41770.map.gz | 11.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-41770-v30.xml emd-41770.xml | 14.8 KB 14.8 KB | Display Display | EMDB header |
Images | emd_41770.png | 73.3 KB | ||
Filedesc metadata | emd-41770.cif.gz | 5.6 KB | ||
Others | emd_41770_half_map_1.map.gz emd_41770_half_map_2.map.gz | 20.7 MB 20.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41770 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41770 | HTTPS FTP |
-Validation report
Summary document | emd_41770_validation.pdf.gz | 730.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_41770_full_validation.pdf.gz | 729.7 KB | Display | |
Data in XML | emd_41770_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | emd_41770_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41770 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41770 | HTTPS FTP |
-Related structure data
Related structure data | 8tzvMC 8uauC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_41770.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_41770_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_41770_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Arginyl-tRNA--protein transferase 1
Entire | Name: Arginyl-tRNA--protein transferase 1 |
---|---|
Components |
|
-Supramolecule #1: Arginyl-tRNA--protein transferase 1
Supramolecule | Name: Arginyl-tRNA--protein transferase 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1
Macromolecule | Name: Isoform ATE1-2 of Arginyl-tRNA--protein transferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 59.132898 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: 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 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 34.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 228665 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |