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Open data
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Basic information
Entry | Database: PDB / ID: 5m5h | |||||||||
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Title | RIBOSOME-BOUND YIDC INSERTASE | |||||||||
![]() | Membrane protein insertase YidC | |||||||||
![]() | PROTEIN TRANSPORT / membrane protein / nanodisc / ribosome ligand | |||||||||
Function / homology | ![]() protein localization to chloroplast / protein insertion into membrane from inner side / membrane insertase activity / thylakoid membrane organization / cell envelope Sec protein transport complex / protein transport by the Sec complex / protein insertion into membrane / protein transport / protein folding / protein-containing complex assembly ...protein localization to chloroplast / protein insertion into membrane from inner side / membrane insertase activity / thylakoid membrane organization / cell envelope Sec protein transport complex / protein transport by the Sec complex / protein insertion into membrane / protein transport / protein folding / protein-containing complex assembly / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Kedrov, A. / Wickles, S. / Crevenna, A.H. / van der Sluis, E. / Buschauer, R. / Berninghausen, O. / Lamb, D.C. / Beckmann, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Dynamics of the YidC:Ribosome Complex during Membrane Protein Biogenesis. Authors: Alexej Kedrov / Stephan Wickles / Alvaro H Crevenna / Eli O van der Sluis / Robert Buschauer / Otto Berninghausen / Don C Lamb / Roland Beckmann / ![]() Abstract: Members of the YidC/Oxa1/Alb3 family universally facilitate membrane protein biogenesis, via mechanisms that have thus far remained unclear. Here, we investigated two crucial functional aspects: the ...Members of the YidC/Oxa1/Alb3 family universally facilitate membrane protein biogenesis, via mechanisms that have thus far remained unclear. Here, we investigated two crucial functional aspects: the interaction of YidC with ribosome:nascent chain complexes (RNCs) and the structural dynamics of RNC-bound YidC in nanodiscs. We observed that a fully exposed nascent transmembrane domain (TMD) is required for high-affinity YidC:RNC interactions, while weaker binding may already occur at earlier stages of translation. YidC efficiently catalyzed the membrane insertion of nascent TMDs in both fluid and gel phase membranes. Cryo-electron microscopy and fluorescence analysis revealed a conformational change in YidC upon nascent chain insertion: the essential TMDs 2 and 3 of YidC were tilted, while the amphipathic helix EH1 relocated into the hydrophobic core of the membrane. We suggest that EH1 serves as a mechanical lever, facilitating a coordinated movement of YidC TMDs to trigger the release of nascent chains into the membrane. | |||||||||
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 | ![]() | 46.6 KB | Display | ![]() |
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PDB format | ![]() | 28.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 704.8 KB | Display | ![]() |
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Full document | ![]() | 711.6 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4155MC 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
#1: Protein | Mass: 61872.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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: Ribosome-bound YidC insertase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: OTHER / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: OTHER |
Image recording | Electron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
EM software | Name: CTFFIND / Version: 4 / Category: CTF correction |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42658 / Symmetry type: POINT |