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- PDB-7xjz: Cryo-EM strucrture of Oryza sativa plastid glycyl-tRNA synthetase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xjz | |||||||||
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Title | Cryo-EM strucrture of Oryza sativa plastid glycyl-tRNA synthetase in complex with tRNA (tRNA binding state) | |||||||||
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![]() | LIGASE/RNA / GlyRS2 / Glycine-tRNA ligase / tRNA selection / GlyRS tRNA complex / chloroplasts / LIGASE / LIGASE-RNA complex | |||||||||
Function / homology | ![]() arginine-tRNA ligase activity / arginyl-tRNA aminoacylation / glycyl-tRNA aminoacylation / glycine-tRNA ligase / glycine-tRNA ligase activity / embryo development ending in seed dormancy / regulation of embryonic development / chloroplast / mitochondrion / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Yu, Z. / Wu, Z. / Li, Y. / Lu, G. / Lin, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of a two-step tRNA recognition mechanism for plastid glycyl-tRNA synthetase. Authors: Zhaoli Yu / Zihan Wu / Ye Li / Qiang Hao / Xiaofeng Cao / Gregor M Blaha / Jinzhong Lin / Guoliang Lu / ![]() ![]() Abstract: Two types of glycyl-tRNA synthetase (GlyRS) are known, the α2 and the α2β2 GlyRSs. Both types of synthetase employ a class II catalytic domain to aminoacylate tRNAGly. In plastids and some ...Two types of glycyl-tRNA synthetase (GlyRS) are known, the α2 and the α2β2 GlyRSs. Both types of synthetase employ a class II catalytic domain to aminoacylate tRNAGly. In plastids and some bacteria, the α and β subunits are fused and are designated as (αβ)2 GlyRSs. While the tRNA recognition and aminoacylation mechanisms are well understood for α2 GlyRSs, little is known about the mechanisms for α2β2/(αβ)2 GlyRSs. Here we describe structures of the (αβ)2 GlyRS from Oryza sativa chloroplast by itself and in complex with cognate tRNAGly. The set of structures reveals that the U-shaped β half of the synthetase selects the tRNA in a two-step manner. In the first step, the synthetase engages the elbow and the anticodon base C35 of the tRNA. In the second step, the tRNA has rotated ∼9° toward the catalytic centre. The synthetase probes the tRNA for the presence of anticodon base C36 and discriminator base C73. This intricate mechanism enables the tRNA to access the active site of the synthetase from a direction opposite to that of most other class II synthetases. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 224.4 KB | Display | ![]() |
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PDB format | ![]() | 168 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 33238MC ![]() 7xjyC ![]() 7xk0C ![]() 7xk1C ![]() 8h1cC 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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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 117050.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Os06g0103600, OsJ_19814, OSNPB_060103600 / Plasmid: pET26 / Production host: ![]() ![]() |
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#2: RNA chain | Mass: 23906.104 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: in vitro transcription vector pT7-TP(deltai) (others) |
Has ligand of interest | N |
-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
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179986 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE | ||||||||||||||||||||||||
Refine LS restraints |
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