+Open data
-Basic information
Entry | Database: PDB / ID: 5m5h | |||||||||
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Title | RIBOSOME-BOUND YIDC INSERTASE | |||||||||
Components | Membrane protein insertase YidC | |||||||||
Keywords | PROTEIN TRANSPORT / membrane protein / nanodisc / ribosome ligand | |||||||||
Function / homology | Function and homology information protein insertion into membrane from inner side / membrane insertase activity / 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 | Escherichia coli (E. coli) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Kedrov, A. / Wickles, S. / Crevenna, A.H. / van der Sluis, E. / Buschauer, R. / Berninghausen, O. / Lamb, D.C. / Beckmann, R. | |||||||||
Funding support | Germany, 2items
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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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5m5h.cif.gz | 46.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m5h.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 5m5h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m5h_validation.pdf.gz | 704.8 KB | Display | wwPDB validaton report |
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Full document | 5m5h_full_validation.pdf.gz | 711.6 KB | Display | |
Data in XML | 5m5h_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5m5h_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/5m5h ftp://data.pdbj.org/pub/pdb/validation_reports/m5/5m5h | HTTPS FTP |
-Related structure data
Related structure data | 4155MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Escherichia coli (E. coli) / Gene: yidC, ECS88_4129 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MGC7, UniProt: P25714*PLUS |
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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 |
-Sample preparation
Component | Name: Ribosome-bound YidC insertase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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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
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) |
-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 |