[English] 日本語
Yorodumi- PDB-5jb3: Cryo-EM structure of a full archaeal ribosomal translation initia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jb3 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-REMOTE conformation | ||||||
Components |
| ||||||
Keywords | TRANSLATION | ||||||
Function / homology | Function and homology information translation reinitiation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translational initiation / translation initiation factor activity / cytosolic ribosome ...translation reinitiation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translational initiation / translation initiation factor activity / cytosolic ribosome / rRNA processing / ribosome binding / ribosome biogenesis / small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / GTPase activity / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Pyrococcus abyssi GE5 (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.34 Å | ||||||
Authors | Coureux, P.-D. / Schmitt, E. / Mechulam, Y. | ||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Cryo-EM study of start codon selection during archaeal translation initiation. Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Auriane Monestier / Eric Larquet / Lionel Cladière / Bruno P Klaholz / Emmanuelle Schmitt / Yves Mechulam / Abstract: Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNA) and mRNA bound to the small ribosomal ...Eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aIF1, e/aIF1A, the ternary complex (TC, e/aIF2-GTP-Met-tRNA) and mRNA bound to the small ribosomal subunit. e/aIF2 plays a crucial role in this process but how this factor controls start codon selection remains unclear. Here, we present cryo-EM structures of the full archaeal 30S initiation complex showing two conformational states of the TC. In the first state, the TC is bound to the ribosome in a relaxed conformation with the tRNA oriented out of the P site. In the second state, the tRNA is accommodated within the peptidyl (P) site and the TC becomes constrained. This constraint is compensated by codon/anticodon base pairing, whereas in the absence of a start codon, aIF2 contributes to swing out the tRNA. This spring force concept highlights a mechanism of codon/anticodon probing by the initiator tRNA directly assisted by aIF2. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5jb3.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5jb3.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 5jb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/5jb3 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/5jb3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8148MC 8149C 5jbhC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-RNA chain , 3 types, 3 molecules 245
#1: RNA chain | Mass: 493106.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: 16S model from Pyrococcus furiosus (PDB code 4V6U) used for fitting Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: GenBank: 5457433 |
---|---|
#30: RNA chain | Mass: 24488.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: tRNA model from Sulfolobus solfataricus (PDB code 3V11) used for fitting Source: (gene. exp.) Escherichia coli (E. coli) / Variant: A1U72 / Production host: Escherichia coli (E. coli) |
#31: RNA chain | Mass: 8394.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea) |
+30S ribosomal protein ... , 27 types, 27 molecules MNQRABVWZDEFGIJCLOPSTUXYHK0
-Protein , 3 types, 3 molecules 316
#18: Protein | Mass: 13414.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: 50S ribosomal protein L7AE model from Pyrococcus furiosus (PDB code 4V6U) used for fitting Source: (natural) Pyrococcus abyssi GE5 (archaea) / References: UniProt: P62008, UniProt: Q8U160*PLUS |
---|---|
#32: Protein | Mass: 11621.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Gene: MJ0463 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57902*PLUS |
#33: Protein | Mass: 13078.265 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 |
-Translation initiation factor 2 subunit ... , 3 types, 3 molecules 789
#34: Protein | Mass: 45849.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: aIF2-gamma model from Sulfolobus solfataricus (PDB code 3V11) used for fitting Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Gene: eif2g, SSO0412 / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5*PLUS |
---|---|
#35: Protein | Mass: 15942.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: aIF2-beta model from Sulfolobus solfataricus (PDB code 3V11) used for fitting Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Gene: eif2b, aif2b, SSO2381 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W59*PLUS |
#36: Protein | Mass: 30432.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: aIF2-alpha model from Sulfolobus solfataricus (PDB code 3V11) used for fitting Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Gene: eif2a, aif2a, SSO1050 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97Z79*PLUS |
-Non-polymers , 4 types, 4 molecules
#37: Chemical | ChemComp-MET / |
---|---|
#38: Chemical | ChemComp-MG / |
#39: Chemical | ChemComp-GNP / |
#40: Chemical | ChemComp-ZN / |
-Details
Sequence details | the pyrococcus furiosus model of the 30S subunit was fitted in the electron density map of the 30S ...the pyrococcus furiosus model of the 30S subunit was fitted in the electron density map of the 30S subunit from pyrococcus abyssi. This explain the alignment mismatches |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 30S archaeal translation initiation complex / Type: COMPLEX / Entity ID: #1-#36 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Value: 0.982 MDa / Experimental value: YES |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 44 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 5.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12600 / Symmetry type: POINT |