|Entry||Database: EMDB / ID: 4155|
|Title||Ribosome-bound membrane insertase YidC|
|Sample||Complex of translationally-stalled ribosome and membrane-embedded YidC insertase:|
|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
|Source||Escherichia coli (E. coli)|
|Method||single particle reconstruction / cryo EM / 4.5 Å resolution|
|Authors||Kedrov A / Wickles S / Crevenna AH / van der Sluis EO / Buschauer R / Berninghausen O / Lamb DC / 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.
|Validation Report||PDB-ID: 5m5h|
SummaryFull reportAbout validation report
|Date||Deposition: Oct 20, 2016 / Header (metadata) release: Nov 23, 2016 / Map release: Dec 14, 2016 / Last update: Aug 2, 2017|
|Structure viewer||EM map: |
Downloads & links
|File||emd_4155.map.gz (map file in CCP4 format, 364501 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.084 Å|
CCP4 map header:
-Entire Complex of translationally-stalled ribosome and membrane-embedded...
|Entire||Name: Complex of translationally-stalled ribosome and membrane-embedded YidC insertase|
Number of components: 1
-Component #1: protein, Complex of translationally-stalled ribosome and membrane...
|Protein||Name: Complex of translationally-stalled ribosome and membrane-embedded YidC insertase|
Recombinant expression: No
|Source||Species: Escherichia coli (E. coli)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Vector: pTrc99A|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: 150 mM KOAc, 5 mM Mg(OAc)2, 25 mM HEPES pH 7.2|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 24 e/Å2 / Illumination mode: SPOT SCAN|
|Lens||Imaging mode: OTHER|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 42658|
|3D reconstruction||Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator
-Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
- Result of Omokage search can be filtered by keywords and the database types
Related info.: Omokage search
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi