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- PDB-5nco: Quaternary complex between SRP, SR, and SecYEG bound to the trans... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nco | |||||||||
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Title | Quaternary complex between SRP, SR, and SecYEG bound to the translating ribosome | |||||||||
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![]() | RIBOSOME / SRP / Sec translocon / SRP receptor / quaternary complex | |||||||||
Function / homology | ![]() protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / protein-transporting ATPase activity / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane ...protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / protein-transporting ATPase activity / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein targeting to membrane / stringent response / protein transmembrane transporter activity / protein secretion / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / protein targeting / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / negative regulation of DNA-templated DNA replication initiation / mRNA regulatory element binding translation repressor activity / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / intracellular protein transport / response to radiation / cytoplasmic side of plasma membrane / mRNA 5'-UTR binding / large ribosomal subunit / ribosome binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / GTPase activity / negative regulation of DNA-templated transcription / mRNA binding / GTP binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||
![]() | Jomaa, A. / Hwang Fu, Y. / Boerhinger, D. / Leibundgut, M. / Shan, S.O. / Ban, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome. Authors: Ahmad Jomaa / Yu-Hsien Hwang Fu / Daniel Boehringer / Marc Leibundgut / Shu-Ou Shan / Nenad Ban / ![]() ![]() Abstract: During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the ...During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the membrane, where the signal peptide is transferred to the translocon. Using electron cryo-microscopy, we have determined the structure of a quaternary complex of the translating Escherichia coli ribosome, the SRP-SR in the 'activated' state and the translocon. Our structure, supported by biochemical experiments, reveals that the SRP RNA adopts a kinked and untwisted conformation to allow repositioning of the 'activated' SRP-SR complex on the ribosome. In addition, we observe the translocon positioned through interactions with the SR in the vicinity of the ribosome exit tunnel where the signal sequence is extending beyond its hydrophobic binding groove of the SRP M domain towards the translocon. Our study provides new insights into the mechanism of signal sequence transfer from the SRP to the translocon. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.5 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3617MC 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 , 4 types, 4 molecules 12AB
#1: RNA chain | Mass: 33611.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: RNA chain | Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: RNA chain | Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: RNA chain | Mass: 38790.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
+50S ribosomal protein ... , 30 types, 30 molecules CDEFGHIJKLMNOPQRSTUVWXYZabcdef
-Protein translocase subunit ... , 2 types, 2 molecules gh
#35: Protein | Mass: 45627.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#36: Protein | Mass: 6241.415 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Signal recognition particle ... , 2 types, 2 molecules il
#37: Protein | Mass: 48514.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#40: Protein | Mass: 29443.721 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Protein/peptide , 2 types, 2 molecules jk
#38: Protein | Mass: 7234.632 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#39: Protein/peptide | Mass: 2276.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 7 molecules ![](data/chem/img/ZN.gif)
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![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/ALF.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
#41: Chemical | ChemComp-ZN / | ||||
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#42: Chemical | #43: Chemical | #44: Chemical | |
-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
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Molecular weight | Value: 2.7 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 / Calibrated magnification: 100719 X / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 85 K / Temperature (min): 78 K |
Image recording | Electron dose: 20 e/Å2 / Detector mode: OTHER / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
EM software |
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CTF correction | Details: After 3D reconstruction 3D maps were sharpened / Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1029950 | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13926 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.8 Å |