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- PDB-7n1p: Elongating 70S ribosome complex in a classical pre-translocation ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n1p | ||||||
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Title | Elongating 70S ribosome complex in a classical pre-translocation (PRE-C) conformation | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rundlet, E.J. / Holm, M. / Schacherl, M. / Natchiar, S.K. / Altman, R.B. / Spahn, C.M.T. / Myasnikov, A.G. / Blanchard, S.C. | ||||||
![]() | ![]() Title: Structural basis of early translocation events on the ribosome. Authors: Emily J Rundlet / Mikael Holm / Magdalena Schacherl / S Kundhavai Natchiar / Roger B Altman / Christian M T Spahn / Alexander G Myasnikov / Scott C Blanchard / ![]() ![]() Abstract: Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around ...Peptide-chain elongation during protein synthesis entails sequential aminoacyl-tRNA selection and translocation reactions that proceed rapidly (2-20 per second) and with a low error rate (around 10 to 10 at each step) over thousands of cycles. The cadence and fidelity of ribosome transit through mRNA templates in discrete codon increments is a paradigm for movement in biological systems that must hold for diverse mRNA and tRNA substrates across domains of life. Here we use single-molecule fluorescence methods to guide the capture of structures of early translocation events on the bacterial ribosome. Our findings reveal that the bacterial GTPase elongation factor G specifically engages spontaneously achieved ribosome conformations while in an active, GTP-bound conformation to unlock and initiate peptidyl-tRNA translocation. These findings suggest that processes intrinsic to the pre-translocation ribosome complex can regulate the rate of protein synthesis, and that energy expenditure is used later in the translocation mechanism than previously proposed. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 3.3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 208.8 KB | Display | |
Data in CIF | ![]() | 334.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24120MC ![]() 7n2cC ![]() 7n2uC ![]() 7n2vC ![]() 7n30C ![]() 7n31C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 6 types, 6 molecules 16mR235PtDt
#1: RNA chain | Mass: 499873.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 16S rRNA / Source: (natural) ![]() ![]() ![]() |
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#22: RNA chain | ![]() Mass: 19128.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
#23: RNA chain | ![]() Mass: 941795.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#24: RNA chain | ![]() Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#56: RNA chain | ![]() Mass: 24703.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: tRNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
#58: RNA chain | ![]() Mass: 24733.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
-30S ribosomal protein ... , 20 types, 20 molecules SBSCSDSESFSGSHSISJSKSLSMSNSOSPSQSRSSSTSU
#2: Protein | ![]() Mass: 26781.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal protein S2 / Source: (natural) ![]() ![]() ![]() |
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#3: Protein | ![]() Mass: 26031.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal protein S3 / Source: (natural) ![]() ![]() ![]() |
#4: Protein | ![]() Mass: 23514.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S4 / Source: (natural) ![]() ![]() ![]() |
#5: Protein | ![]() Mass: 17629.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S5 / Source: (natural) ![]() ![]() ![]() |
#6: Protein | ![]() Mass: 15727.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S6 / Source: (natural) ![]() ![]() ![]() |
#7: Protein | ![]() Mass: 20055.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S7 / Source: (natural) ![]() ![]() ![]() |
#8: Protein | ![]() Mass: 14146.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S8 / Source: (natural) ![]() ![]() ![]() |
#9: Protein | ![]() Mass: 14886.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S10 / Source: (natural) ![]() ![]() ![]() |
#10: Protein | ![]() Mass: 11755.597 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S10 / Source: (natural) ![]() ![]() ![]() |
#11: Protein | ![]() Mass: 13870.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S11 / Source: (natural) ![]() ![]() ![]() |
#12: Protein | ![]() Mass: 13814.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S12 / Source: (natural) ![]() ![]() ![]() |
#13: Protein | ![]() Mass: 13128.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S13 / Source: (natural) ![]() ![]() ![]() |
#14: Protein | ![]() Mass: 11606.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S14 / Source: (natural) ![]() ![]() ![]() |
#15: Protein | ![]() Mass: 10290.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S15 / Source: (natural) ![]() ![]() ![]() |
#16: Protein | ![]() Mass: 9207.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S16 / Source: (natural) ![]() ![]() ![]() |
#17: Protein | ![]() Mass: 9724.491 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S17 / Source: (natural) ![]() ![]() ![]() |
#18: Protein | ![]() Mass: 9005.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S18 / Source: (natural) ![]() ![]() ![]() |
#19: Protein | ![]() Mass: 10455.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S19 / Source: (natural) ![]() ![]() ![]() |
#20: Protein | ![]() Mass: 9708.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ribosomal Protein S20 / Source: (natural) ![]() ![]() ![]() |
#21: Protein | ![]() Mass: 8524.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
+50S ribosomal protein ... , 31 types, 31 molecules LBLCLDLELFLILJLKLMLNLOLPLQLRLSLTLULVLWLXLYLaLbLcLdLeLfLgLhLiLj
-Protein/peptide , 1 types, 1 molecules Pp
#57: Protein/peptide | Mass: 425.565 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 484 molecules 










#59: Chemical | ChemComp-PUT / ![]() #60: Chemical | ChemComp-MG / #61: Chemical | #62: Chemical | ![]() #63: Chemical | ChemComp-SPD / ![]() #64: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 5.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K |
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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![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 87 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
CTF correction![]() | Type: PHASE FLIPPING ONLY |
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3D reconstruction![]() | Resolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109769 / Symmetry type: POINT |
Atomic model building | Protocol: OTHER / Space: REAL |