[English] 日本語
Yorodumi- PDB-6swc: IC2B model of cryo-EM structure of a full archaeal ribosomal tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6swc | ||||||
---|---|---|---|---|---|---|---|
Title | IC2B model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi | ||||||
Components |
| ||||||
Keywords | RIBOSOME / Translation initiation / cryo-EM / tRNA / evolution / archaea / rRNA modifications | ||||||
Function / homology | Function and homology information selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translation initiation factor binding ...selenocysteine metabolic process / selenocysteine incorporation / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / formation of translation preinitiation complex / ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / translation initiation factor binding / translational initiation / translation initiation factor activity / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / positive regulation of apoptotic signaling pathway / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Pyrococcus abyssi (archaea) Pyrococcus abyssi GE5 (archaea) Saccharolobus solfataricus (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Coureux, P.-D. / Mechulam, Y. / Schmitt, E. | ||||||
Funding support | France, 1items
| ||||||
Citation | Journal: Commun Biol / Year: 2020 Title: Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation. Authors: Pierre-Damien Coureux / Christine Lazennec-Schurdevin / Sophie Bourcier / Yves Mechulam / Emmanuelle Schmitt / Abstract: Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP: ...Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNA complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6swc.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6swc.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6swc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6swc_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6swc_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6swc_validation.xml.gz | 161.5 KB | Display | |
Data in CIF | 6swc_validation.cif.gz | 265.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/6swc ftp://data.pdbj.org/pub/pdb/validation_reports/sw/6swc | HTTPS FTP |
-Related structure data
Related structure data | 10322MC 6sw9C 6swdC 6sweC 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 254
#1: RNA chain | Mass: 487700.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrococcus abyssi GE5 (archaea) |
---|---|
#30: RNA chain | Mass: 6448.871 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus abyssi GE5 (archaea) |
#31: RNA chain | Mass: 24504.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Variant: A1U72 / Production host: Escherichia coli (E. coli) |
+30S ribosomal protein ... , 26 types, 26 molecules ABDEFGHIJKLMNOPQRSTUVWXYZ0
-Protein , 3 types, 3 molecules C36
#4: Protein | Mass: 7163.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Strain: GE5 / Orsay / References: UniProt: G8ZFK7 |
---|---|
#29: Protein | Mass: 13442.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Strain: GE5 / Orsay / References: UniProt: P62008 |
#32: Protein | Mass: 13078.265 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (strain GE5 / Orsay) (archaea) Strain: GE5 / Orsay / Gene: eIF1A, aif1A, PYRAB05910, PAB2441 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V138 |
-Translation initiation factor 2 subunit ... , 3 types, 3 molecules 789
#33: Protein | Mass: 45849.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Model from high resolution structures of aIF2 gamma of Saccharolobus solfataricus Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q980A5*PLUS |
---|---|
#34: Protein | Mass: 15942.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Model from high resolution structures of aIF2 beta of Saccharolobus solfataricus Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97W59*PLUS |
#35: Protein | Mass: 30432.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Model from high resolution structures of aIF2 alpha of Saccharolobus solfataricus Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: eif2a, aif2a, SSO1050 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97Z79 |
-Non-polymers , 5 types, 84 molecules
#36: Chemical | ChemComp-MG / #37: Chemical | ChemComp-ZN / #38: Chemical | ChemComp-MET / | #39: Chemical | ChemComp-GNP / | #40: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 1.05 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 6.7 | ||||||||||||||||||||||||||||||||||||||||||||||||
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 FIELD |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|