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Yorodumi- PDB-5ot7: Elongation factor G-ribosome complex captures in the absence of i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ot7 | |||||||||
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Title | Elongation factor G-ribosome complex captures in the absence of inhibitors. | |||||||||
Components |
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Keywords | RIBOSOME / Elongation factor G / Translation / Translocation | |||||||||
Function / homology | Function and homology information translation elongation factor activity / large ribosomal subunit / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit ...translation elongation factor activity / large ribosomal subunit / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / zinc ion binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Thermus thermophilus (bacteria) Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Mace, K. / Giudice, E. / Chat, S. / Gillet, R. | |||||||||
Funding support | France, 2items
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Citation | Journal: Nucleic Acids Res / Year: 2018 Title: The structure of an elongation factor G-ribosome complex captured in the absence of inhibitors. Authors: Kevin Macé / Emmanuel Giudice / Sophie Chat / Reynald Gillet / Abstract: During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome ...During translation's elongation cycle, elongation factor G (EF-G) promotes messenger and transfer RNA translocation through the ribosome. Until now, the structures reported for EF-G-ribosome complexes have been obtained by trapping EF-G in the ribosome. These results were based on use of non-hydrolyzable guanosine 5'-triphosphate (GTP) analogs, specific inhibitors or a mutated EF-G form. Here, we present the first cryo-electron microscopy structure of EF-G bound to ribosome in the absence of an inhibitor. The structure reveals a natural conformation of EF-G·GDP in the ribosome, with a previously unseen conformation of its third domain. These data show how EF-G must affect translocation, and suggest the molecular mechanism by which fusidic acid antibiotic prevents the release of EF-G after GTP hydrolysis. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ot7.cif.gz | 3.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ot7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5ot7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ot7_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5ot7_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5ot7_validation.xml.gz | 244.9 KB | Display | |
Data in CIF | 5ot7_validation.cif.gz | 423.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/5ot7 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/5ot7 | HTTPS FTP |
-Related structure data
Related structure data | 3852MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 5 types, 5 molecules 12345
#1: RNA chain | Mass: 489331.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: GenBank: 55771382 |
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#2: RNA chain | Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: GenBank: 1319589919 |
#3: RNA chain | Mass: 4889.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
#4: RNA chain | Mass: 943515.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: GenBank: 55771382 |
#5: RNA chain | Mass: 38553.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: GenBank: 55771382 |
+50S ribosomal protein ... , 30 types, 30 molecules 67VWXYZabcdefghijkopqrstuvwxyz
-30S ribosomal protein ... , 20 types, 20 molecules ABCDEFGHIJKLMNOPQRST
#8: Protein | Mass: 27116.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P80371 |
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#9: Protein | Mass: 22975.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P80372 |
#10: Protein | Mass: 24242.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P80373 |
#11: Protein | Mass: 16460.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: Q5SHQ5 |
#12: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: Q5SLP8 |
#13: Protein | Mass: 17919.775 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P17291 |
#14: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P0DOY9 |
#15: Protein | Mass: 14279.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P80374 |
#16: Protein | Mass: 11398.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: Q5SHN7 |
#17: Protein | Mass: 12606.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P80376 |
#18: Protein | Mass: 13875.388 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: Q5SHN3 |
#19: Protein | Mass: 13494.739 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P80377 |
#20: Protein | Mass: 7027.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P0DOY6 |
#21: Protein | Mass: 10447.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: Q5SJ76 |
#22: Protein | Mass: 9995.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: Q5SJH3 |
#23: Protein | Mass: 11880.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P0DOY7 |
#24: Protein | Mass: 8155.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: Q5SLQ0 |
#25: Protein | Mass: 9961.599 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: Q5SHP2 |
#26: Protein | Mass: 10921.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: P80380 |
#27: Protein/peptide | Mass: 3089.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) References: UniProt: Q5SIH3 |
-Protein , 1 types, 1 molecules U
#28: Protein | Mass: 76547.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: fusA, fus, TTHA1695 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SHN5 |
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-Ribosomal protein ... , 3 types, 3 molecules lmn
#45: Protein | Mass: 11109.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) |
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#46: Protein | Mass: 11932.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) |
#47: Protein | Mass: 6060.462 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) |
-Non-polymers , 3 types, 466 molecules
#60: Chemical | ChemComp-MG / #61: Chemical | #62: Chemical | ChemComp-GDP / | |
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-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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 303 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 / Nominal magnification: 59000 X / Calibrated magnification: 120443 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 2700 nm / Cs: 0.0023 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1 sec. / Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 949 |
EM imaging optics | Spherical aberration corrector: CS-corrected |
Image scans | Movie frames/image: 7 / Used frames/image: 1-7 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 96509 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32383 / Algorithm: BACK PROJECTION Details: Resolution : 5.36 Resolution (masked and sharpened) : 3.8 Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: each ribosomal rna and protein was first rigid body fitted in the map using UCSF chimera. The missing componant (mRNA and bL9) were then added and fitted. the quality of the fitting was then ...Details: each ribosomal rna and protein was first rigid body fitted in the map using UCSF chimera. The missing componant (mRNA and bL9) were then added and fitted. the quality of the fitting was then assesed and adjust manually, residue per residue using coot. the RNA confomation were ajusted with the ERRASER modul (in Phenix). The final model was refined using phenix real space refinement procedure. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.8 Å |