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- PDB-5m5h: RIBOSOME-BOUND YIDC INSERTASE -

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Basic information

Entry
Database: PDB / ID: 5m5h
TitleRIBOSOME-BOUND YIDC INSERTASE
ComponentsMembrane protein insertase YidCBiological membrane
KeywordsPROTEIN 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
Membrane insertase YidC, N-terminal / YidC, periplasmic domain superfamily / YidC periplasmic domain / : / Membrane insertase YidC / Membrane insertase YidC/Oxa1, C-terminal / 60Kd inner membrane protein / Membrane insertase YidC/ALB3/OXA1/COX18
Similarity search - Domain/homology
Membrane protein insertase YidC / Membrane protein insertase YidC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKedrov, A. / Wickles, S. / Crevenna, A.H. / van der Sluis, E. / Buschauer, R. / Berninghausen, O. / Lamb, D.C. / Beckmann, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research CouncilERC-2011-ADG "CRYOTRANSLATION" Germany
German Research FoundationKE 1879/3-1 Germany
CitationJournal: 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
DepositionOct 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.name / _em_software.version
Revision 1.3Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Assembly

Deposited unit
A: Membrane protein insertase YidC


Theoretical massNumber of molelcules
Total (without water)61,8731
Polymers61,8731
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8680 Å2
MethodPISA

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Components

#1: Protein Membrane protein insertase YidC / Biological membrane / Foldase YidC / Membrane integrase YidC / Membrane protein YidC


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ribosome-bound YidC insertase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pTrc99A-YidC
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER
Image recordingElectron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM softwareName: CTFFIND / Version: 4 / Category: CTF correction
CTF correctionType: NONE
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42658 / Symmetry type: POINT

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