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- PDB-7n2v: Elongating 70S ribosome complex in a spectinomycin-stalled interm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7n2v | ||||||
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Title | Elongating 70S ribosome complex in a spectinomycin-stalled intermediate state of translocation bound to EF-G in an active, GTP conformation (INT1) | ||||||
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![]() | RIBOSOME / Elongation complex / tRNA / mRNA / translocation / EF-G & GTP | ||||||
Function / homology | ![]() negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation ...negative regulation of cytoplasmic translational initiation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translation elongation factor activity / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / translational initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / assembly of large subunit precursor of preribosome / DNA endonuclease activity / transcription elongation factor complex / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / 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 / tRNA binding / cytoplasmic translation / molecular adaptor activity / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å | ||||||
![]() | Rundlet, E.J. / Holm, M. / Schacherl, M. / Natchiar, K.S. / 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. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 204.8 KB | Display | |
Data in CIF | ![]() | 378.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24134MC ![]() 7n1pC ![]() 7n2cC ![]() 7n2uC ![]() 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: 497391.906 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 / Details: mRNA / Source: (synth.) ![]() ![]() |
#23: RNA chain | Mass: 941812.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 23S rRNA / Source: (natural) ![]() ![]() |
#24: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 5S rRNA / Source: (natural) ![]() ![]() |
#58: RNA chain | Mass: 34369.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: tRNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#59: RNA chain | Mass: 34451.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: tRNA / 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 S9 / 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 / Details: Ribosomal Protein S21 / Source: (natural) ![]() ![]() |
+50S ribosomal protein ... , 31 types, 31 molecules LBLCLDLELFLILJLKLMLNLOLPLQLRLSLTLULVLWLXLYLaLbLcLdLeLfLgLhLiLj
-Protein / Protein/peptide , 2 types, 2 molecules EFPp
#56: Protein | Mass: 77632.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Elongation factor (EF-G) / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#57: Protein/peptide | Mass: 425.565 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Nascent peptide / Source: (natural) ![]() ![]() |
-Non-polymers , 8 types, 398 molecules ![](data/chem/img/SCM.gif)
![](data/chem/img/PUT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PUT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/SPD.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
#60: Chemical | #61: Chemical | ChemComp-PUT / #62: Chemical | ChemComp-MG / #63: Chemical | #64: Chemical | #65: Chemical | #66: Chemical | ChemComp-GTP / | #67: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: Elongating 70S ribosome complex in a spectinomycin-stalled intermediate state of translocation bound to EF-G in an active, GTP conformation (INT1) Type: RIBOSOME / Entity ID: #1-#56, #58, #57, #59 / Source: NATURAL |
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Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5.5 mg/ml / 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 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: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33688 / Symmetry type: POINT |
Atomic model building | Protocol: OTHER / Space: RECIPROCAL |