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Yorodumi- PDB-4v5n: tRNA translocation on the 70S ribosome: the post- translocational... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v5n | ||||||||||||
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Title | tRNA translocation on the 70S ribosome: the post- translocational translocation intermediate TI(POST) | ||||||||||||
Components |
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Keywords | RIBOSOME / TRANSLATION / ELONGATION CYCLE / TRNA TRANSLOCATION | ||||||||||||
Function / homology | Function and homology information ribosome disassembly / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / large ribosomal subunit / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit ...ribosome disassembly / endo-alpha-N-acetylgalactosaminidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / translation elongation factor activity / large ribosomal subunit / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / protein homodimerization activity / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | THERMUS THERMOPHILUS (bacteria) ESCHERICHIA COLI (E. coli) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.6 Å | ||||||||||||
Authors | Ratje, A.H. / Loerke, J. / Mikolajka, A. / Bruenner, M. / Hildebrand, P.W. / Starosta, A.L. / Doenhoefer, A. / Connell, S.R. / Fucini, P. / Mielke, T. ...Ratje, A.H. / Loerke, J. / Mikolajka, A. / Bruenner, M. / Hildebrand, P.W. / Starosta, A.L. / Doenhoefer, A. / Connell, S.R. / Fucini, P. / Mielke, T. / Whitford, P.C. / Onuchic, J.N. / Yu, Y. / Sanbonmatsu, K.Y. / Hartmann, R.K. / Penczek, P.A. / Wilson, D.N. / Spahn, C.M.T. | ||||||||||||
Citation | Journal: Nature / Year: 2010 Title: Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites. Authors: Andreas H Ratje / Justus Loerke / Aleksandra Mikolajka / Matthias Brünner / Peter W Hildebrand / Agata L Starosta / Alexandra Dönhöfer / Sean R Connell / Paola Fucini / Thorsten Mielke / ...Authors: Andreas H Ratje / Justus Loerke / Aleksandra Mikolajka / Matthias Brünner / Peter W Hildebrand / Agata L Starosta / Alexandra Dönhöfer / Sean R Connell / Paola Fucini / Thorsten Mielke / Paul C Whitford / José N Onuchic / Yanan Yu / Karissa Y Sanbonmatsu / Roland K Hartmann / Pawel A Penczek / Daniel N Wilson / Christian M T Spahn / Abstract: The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and ...The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen the A site. The translocation reaction is catalysed by elongation factor G (EF-G) in a GTP-dependent manner. Despite the availability of structures of various EF-G-ribosome complexes, the precise mechanism by which tRNAs move through the ribosome still remains unclear. Here we use multiparticle cryoelectron microscopy analysis to resolve two previously unseen subpopulations within Thermus thermophilus EF-G-ribosome complexes at subnanometre resolution, one of them with a partly translocated tRNA. Comparison of these substates reveals that translocation of tRNA on the 30S subunit parallels the swivelling of the 30S head and is coupled to unratcheting of the 30S body. Because the tRNA maintains contact with the peptidyl-tRNA-binding site (P site) on the 30S head and simultaneously establishes interaction with the exit site (E site) on the 30S platform, a novel intra-subunit 'pe/E' hybrid state is formed. This state is stabilized by domain IV of EF-G, which interacts with the swivelled 30S-head conformation. These findings provide direct structural and mechanistic insight into the 'missing link' in terms of tRNA intermediates involved in the universally conserved translocation process. | ||||||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4v5n.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v5n.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v5n_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4v5n_full_validation.pdf.gz | 4.5 MB | Display | |
Data in XML | 4v5n_validation.xml.gz | 564.5 KB | Display | |
Data in CIF | 4v5n_validation.cif.gz | 825.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/4v5n ftp://data.pdbj.org/pub/pdb/validation_reports/v5/4v5n | HTTPS FTP |
-Related structure data
Related structure data | 1799MUC 1798C 4v5mC 2jl5 2jl7 C: citing same article (ref.) M: map data used to model this data U: unfit; in different coordinate system*YM |
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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 AAAVAXBABB
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: GenBank: 55979969 |
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#22: RNA chain | Mass: 24802.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TRNA WAS COPURIFIED WITH 70S RIBOSOMES / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 |
#23: RNA chain | Mass: 3476.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MRNA WAS COPURIFIED WITH 70S RIBOSOMES / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 |
#35: RNA chain | Mass: 947935.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4 Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969 |
#36: RNA chain | Mass: 39540.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969 |
-30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules ABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU
#2: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80371 |
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#3: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80372 |
#4: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80373 |
#5: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ5 |
#6: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SLP8 |
#7: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P17291 |
#8: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS |
#9: Protein | Mass: 14410.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80374 |
#10: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHN7 |
#11: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80376 |
#12: Protein | Mass: 14637.384 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHN3 |
#13: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80377 |
#14: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS |
#15: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SJ76 |
#16: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SJH3 |
#17: Protein | Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS |
#18: Protein | Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SLQ0 |
#19: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SHP2 |
#20: Protein | Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: P80380 |
#21: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / References: UniProt: Q5SIH3 |
-Protein , 1 types, 1 molecules AY
#24: Protein | Mass: 76977.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PET-46 EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHN5 |
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+50S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules B0B1B2B3B4B5B6B7B8B9BCBDBEBFBGBHBKBLBNBOBPBQBRBSBTBUBVBWBXBYBZ
-Non-polymers , 2 types, 2 molecules
#58: Chemical | ChemComp-FUA / |
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#59: Chemical | ChemComp-GDP / |
-Details
Sequence details | CHAIN V: MRNA WAS COPURIFIED, THEREFORE UNKNOWN SEQUENCE CHAIN X: TRNA WAS COPURIFIED, THEREFORE ...CHAIN V: MRNA WAS COPURIFIED |
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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 | Name: 70S-EFG-GDP-FA COMPLEX / Type: RIBOSOME |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- VITROBOT (FEI) |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Details: LOW-DOSE |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 65520 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Specimen holder | Temperature: 77 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 677 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: DEFOCUS GROUPS | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: MULTIPARTICLE REFINEMENT / Resolution: 7.6 Å / Nominal pixel size: 1.26 Å / Actual pixel size: 1.26 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1799. (DEPOSITION ID: 7584). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Details: METHOD--MDFIT REFINEMENT PROTOCOL--X-RAY | ||||||||||||
Atomic model building |
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Refinement | Highest resolution: 7.6 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.6 Å
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