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Open data
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Basic information
Entry | Database: PDB / ID: 8omr | ||||||
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Title | Human tRNA guanine transglycosylase (TGT) bound to tRNAAsp | ||||||
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![]() | RNA BINDING PROTEIN / RNA modification / transglycosylation / nucleid acid-protein complex / tRNA binding | ||||||
Function / homology | ![]() tRNA-guanosine34 queuine transglycosylase / tRNA modification in the nucleus and cytosol / transferase complex / tRNA modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity ...tRNA-guanosine34 queuine transglycosylase / tRNA modification in the nucleus and cytosol / transferase complex / tRNA modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / mitochondrial outer membrane / tRNA binding / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / mitochondrion / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
![]() | Sievers, K. / Neumann, P. / Susac, L. / Trowitzsch, S. / Tampe, R. / Ficner, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional insights into tRNA recognition by human tRNA guanine transglycosylase. Authors: Katharina Sievers / Piotr Neumann / Lukas Sušac / Stefano Da Vela / Melissa Graewert / Simon Trowitzsch / Dmitri Svergun / Robert Tampé / Ralf Ficner / ![]() Abstract: Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine ...Eukaryotic tRNA guanine transglycosylase (TGT) is an RNA-modifying enzyme which catalyzes the base exchange of the genetically encoded guanine 34 of tRNAs for queuine, a hypermodified 7-deazaguanine derivative. Eukaryotic TGT is a heterodimer comprised of a catalytic and a non-catalytic subunit. While binding of the tRNA anticodon loop to the active site is structurally well understood, the contribution of the non-catalytic subunit to tRNA binding remained enigmatic, as no complex structure with a complete tRNA was available. Here, we report a cryo-EM structure of eukaryotic TGT in complex with a complete tRNA, revealing the crucial role of the non-catalytic subunit in tRNA binding. We decipher the functional significance of these additional tRNA-binding sites, analyze solution state conformation, flexibility, and disorder of apo TGT, and examine conformational transitions upon tRNA binding. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 403.6 KB | Display | ![]() |
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PDB format | ![]() | 324 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 37.8 KB | Display | |
Data in CIF | ![]() | 58 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 16976MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 44251.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Zn ion and 9DG are ligands / Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9BXR0, tRNA-guanosine34 preQ1 transglycosylase | ||||
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#2: Protein | Mass: 46775.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Zn is an ion / Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: RNA chain | Mass: 24148.312 Da / Num. of mol.: 1 / Mutation: U1A, C2G, C3G, G69C, G70C, A71U / Source method: obtained synthetically / Source: (synth.) ![]() | ||||
#4: Chemical | #5: Chemical | ChemComp-9DG / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Ternary complex of human tRNA guanine transglycosylase and tRNAAsp Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm |
Image recording | Average exposure time: 44.46 sec. / Electron dose: 62.1 e/Å2 / Film or detector model: OTHER |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 463140 / Symmetry type: POINT | ||||||||||||||||||||||||
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