|Entry||Database: PDB / ID: 5m5h|
|Title||RIBOSOME-BOUND YIDC INSERTASE|
|Components||Membrane protein insertase YidCBiological membrane|
|Keywords||PROTEIN TRANSPORT / membrane protein / nanodisc / ribosome ligand|
|Function / homology||Membrane insertase YidC / YidC periplasmic domain / Membrane insertase YidC/ALB3/OXA1/COX18 / Membrane insertase YidC, N-terminal / Membrane insertase YidC/Oxa1, C-terminal / Membrane insertase YidC, periplasmic domain / YidC, periplasmic domain superfamily / 60Kd inner membrane protein / membrane insertase activity / protein insertion into membrane ...Membrane insertase YidC / YidC periplasmic domain / Membrane insertase YidC/ALB3/OXA1/COX18 / Membrane insertase YidC, N-terminal / Membrane insertase YidC/Oxa1, C-terminal / Membrane insertase YidC, periplasmic domain / YidC, periplasmic domain superfamily / 60Kd inner membrane protein / membrane insertase activity / protein insertion into membrane / protein-containing complex assembly / protein folding / protein homooligomerization / integral component of plasma membrane / integral component of membrane / plasma membrane / Membrane protein insertase YidC / Membrane protein insertase YidC|
Function and homology information
|Specimen source||Escherichia coli (E. coli)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.5 Å resolution|
|Authors||Kedrov, A. / Wickles, S. / Crevenna, A.H. / van der Sluis, E. / Buschauer, R. / Berninghausen, O. / Lamb, D.C. / Beckmann, R.|
|Citation||Journal: Cell Rep / Year: 2016|
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.
SummaryFull reportAbout validation report
|Date||Deposition: Oct 21, 2016 / Release: Dec 14, 2016|
|Structure viewer||Molecule: |
Downloads & links
A: Membrane protein insertase YidC
|#1: Protein/peptide|| |
Mass: 61872.703 Da / Num. of mol.: 1 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yidC, ECS88_4129 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC7, UniProt: P25714*PLUS
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Component||Name: Ribosome-bound YidC insertase / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT|
|Source (natural)||Organism: Escherichia coli (E. coli)|
|Source (recombinant)||Organism: Escherichia coli (E. coli) / Plasmid: pTrc99A-YidC|
|Buffer solution||pH: 7.2|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope 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)|
|EM software||Name: CTFFIND / Version: 4 / Category: CTF correction|
|CTF correction||Type: NONE|
|3D reconstruction||Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 42658 / Symmetry type: POINT|
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