+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29638 | |||||||||
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Title | CryoEM structure of yeast Arginyltransferase 1 (ATE1) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Arginyltransferase / post-translational modification / enzyme / TRANSFERASE-RNA complex | |||||||||
Function / homology | Function and homology information arginyltransferase / arginyl-tRNA--protein transferase activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Huang W / Zhang Y / Taylor DJ | |||||||||
Funding support | United States, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29638.map.gz | 58.8 MB | EMDB map data format | |
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Header (meta data) | emd-29638-v30.xml emd-29638.xml | 17.1 KB 17.1 KB | Display Display | EMDB header |
Images | emd_29638.png | 56.9 KB | ||
Filedesc metadata | emd-29638.cif.gz | 5.8 KB | ||
Others | emd_29638_additional_1.map.gz emd_29638_half_map_1.map.gz emd_29638_half_map_2.map.gz | 53.5 MB 2.3 MB 2.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29638 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29638 | HTTPS FTP |
-Validation report
Summary document | emd_29638_validation.pdf.gz | 491.6 KB | Display | EMDB validaton report |
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Full document | emd_29638_full_validation.pdf.gz | 491.2 KB | Display | |
Data in XML | emd_29638_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_29638_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29638 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29638 | HTTPS FTP |
-Related structure data
Related structure data | 8fzrMC 8e3sC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29638.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.8726 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Phenix auto-sharpen map
File | emd_29638_additional_1.map | ||||||||||||
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Annotation | Phenix auto-sharpen map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29638_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29638_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : yeast Arginyltransferase 1 bound to Arg tRNA
Entire | Name: yeast Arginyltransferase 1 bound to Arg tRNA |
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Components |
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-Supramolecule #1: yeast Arginyltransferase 1 bound to Arg tRNA
Supramolecule | Name: yeast Arginyltransferase 1 bound to Arg tRNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Arginyl-tRNA--protein transferase 1
Macromolecule | Name: Arginyl-tRNA--protein transferase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: arginyltransferase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 58.001277 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MSDRFVIWAP SMHNEPAAKC GYCHGNKGGN MDQLFALDSW AHRYMNKMDV VKIENCTIGS FVEHMDVATY DRMCNMGFRR SGKFLYKVD PLRNCCRLYT IRTAPQELNM TKELKKCISR FATRITSEDY CPAAVASSDF VGKIVNAEMN SKTFYTRFEP A LYSEEKYH ...String: MSDRFVIWAP SMHNEPAAKC GYCHGNKGGN MDQLFALDSW AHRYMNKMDV VKIENCTIGS FVEHMDVATY DRMCNMGFRR SGKFLYKVD PLRNCCRLYT IRTAPQELNM TKELKKCISR FATRITSEDY CPAAVASSDF VGKIVNAEMN SKTFYTRFEP A LYSEEKYH LFVKYQEKVH QDYNNSPKSF KRFLCDTPFG PEAVLGTQES WEQLNNWQRM KPGEKLKHMG PVHECYYYEG KL IAITVSD ILPSGISSVY FIWDPDYSKW SLGKLSALRD LAIIQRTNLQ YYYLGYYIED CPKMNYKANY GAEVLDVCHS KYI PLKPIQ DMISRGKLFV IGEEETKVTK ELYLVDSETG RGEGFPTDNV VKYKNIAEEI YGVGGCAFKS ANESALELKE LYGI PYEEE DLDTIYHLKE HNGHAPNGIP NVVPGLLPLW ELLDIMQSGK ITDLEGRLFL FEIETEGIRP LINFYSEPPN VKKRI CDVI RLFGFETCMK AVILYSEQM UniProtKB: Arginyl-tRNA--protein transferase 1 |
-Macromolecule #2: Arg tRNA
Macromolecule | Name: Arg tRNA / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 24.789736 KDa |
Sequence | String: GCGCCCUUAG CUCAGUUGGA UAGAGCAACG ACCUUCUAAG UCGUGGGCCG CAGGUUCGAA UCCUGCAGGG CGCGCCA GENBANK: GENBANK: CP026935.2 |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.1 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 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: 25.0 µm / Nominal defocus min: 5.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL / Details: AlphaFold II predicted mode AF-P16639-F1 |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 208051 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |