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Yorodumi- PDB-7zai: Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zai | ||||||
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Title | Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA, mRNA and aIF1A. | ||||||
Components |
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Keywords | TRANSLATION / Initiation complex / translation initiation / small ribosomal subunit / aIF5b | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation ...ribonuclease P activity / tRNA 5'-leader removal / translation initiation factor activity / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi GE5 (archaea) Pyrococcus abyssi (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Coureux, P.D. / Bourgeois, G. / Mechulam, Y. / Schmitt, E. / Kazan, R. | ||||||
Funding support | France, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2022 Title: Role of aIF5B in archaeal translation initiation. Authors: Ramy Kazan / Gabrielle Bourgeois / Christine Lazennec-Schurdevin / Eric Larquet / Yves Mechulam / Pierre-Damien Coureux / Emmanuelle Schmitt / Abstract: In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established ...In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zai.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7zai.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7zai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zai_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7zai_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7zai_validation.xml.gz | 131.3 KB | Display | |
Data in CIF | 7zai_validation.cif.gz | 220.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/7zai ftp://data.pdbj.org/pub/pdb/validation_reports/za/7zai | HTTPS FTP |
-Related structure data
Related structure data | 14581MC 7yypC 7yznC 7zagC 7zahC 7zhgC 7zkiC C: citing same article (ref.) M: map data used to model this data |
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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
-RNA chain , 3 types, 3 molecules 254
#1: RNA chain | Mass: 487993.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: GenBank: 5457433 |
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#30: RNA chain | Mass: 8064.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea) |
#31: RNA chain | Mass: 24833.904 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: GenBank: 1334604293 |
+30S ribosomal protein ... , 25 types, 25 molecules ABDEFGHIJKLMNOPQRSTUVWXYZ
-Protein , 2 types, 2 molecules C6
#4: Protein | Mass: 7163.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: G8ZFK7 |
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#32: Protein | Mass: 15336.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Gene: eIF1A, aif1A, PYRAB05910, PAB2441 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V138 |
-50S ribosomal protein ... , 2 types, 2 molecules 03
#28: Protein/peptide | Mass: 4910.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / References: UniProt: Q8U232 |
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#29: Protein | Mass: 13442.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) / Strain: GE5 / Orsay / References: UniProt: P62008 |
-Non-polymers , 4 types, 448 molecules
#33: Chemical | ChemComp-MG / #34: Chemical | ChemComp-ZN / #35: Chemical | ChemComp-MET / | #36: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Has protein modification | N |
-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: 30S ribosomal subunit with initiation factor 1A, mRNA and initiator tRNA Type: COMPLEX / Entity ID: #1-#32 / Source: NATURAL |
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Source (natural) | Organism: Pyrococcus abyssi GE5 (archaea) |
Buffer solution | pH: 6.7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS 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: 800 nm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 39 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: PHENIX / Category: model refinement | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2000000 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 382130 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 7ZHG Accession code: 7ZHG / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refine LS restraints |
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