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- PDB-4utq: A structural model of the active ribosome-bound membrane protein ... -

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Basic information

Entry
Database: PDB / ID: 4utq
TitleA structural model of the active ribosome-bound membrane protein insertase YidC
Components
  • ATP SYNTHASE SUBUNIT C
  • MEMBRANE PROTEIN INSERTASE YIDC
KeywordsPROTEIN TRANSPORT / PROTEIN TRANSLOCATION / BIOINFORMATICS / MD SIMULATION / MEMBRANE
Function / homology
Function and homology information


: / membrane insertase activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / protein insertion into membrane / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex ...: / membrane insertase activity / cell envelope Sec protein transport complex / protein transport by the Sec complex / proton motive force-driven plasma membrane ATP synthesis / proton motive force-driven ATP synthesis / protein insertion into membrane / proton-transporting two-sector ATPase complex, proton-transporting domain / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / protein folding / protein-containing complex assembly / lipid binding / 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 / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C ...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 / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C
Similarity search - Domain/homology
Membrane protein insertase YidC / ATP synthase subunit c
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsWickles, S. / Singharoy, A. / Andreani, J. / Seemayer, S. / Bischoff, L. / Berninghausen, O. / Soeding, J. / Schulten, K. / vanderSluis, E.O. / Beckmann, R.
CitationJournal: Elife / Year: 2014
Title: A structural model of the active ribosome-bound membrane protein insertase YidC.
Authors: Stephan Wickles / Abhishek Singharoy / Jessica Andreani / Stefan Seemayer / Lukas Bischoff / Otto Berninghausen / Johannes Soeding / Klaus Schulten / Eli O van der Sluis / Roland Beckmann /
Abstract: The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a ...The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.
History
DepositionJul 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: MEMBRANE PROTEIN INSERTASE YIDC
Z: ATP SYNTHASE SUBUNIT C


Theoretical massNumber of molelcules
Total (without water)69,8362
Polymers69,8362
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein MEMBRANE PROTEIN INSERTASE YIDC / FOLDASE YIDC / INNER MEMBRANE PROTEIN YIDC / MEMBRANE INTEGRASE YIDC / OXA1EC


Mass: 61576.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P25714
#2: Protein ATP SYNTHASE SUBUNIT C / ATP SYNTHASE F(0) SECTOR SUBUNIT C / DICYCLOHEXYLCARBODIIMIDE-BINDING PROTEIN / F-TYPE ATPASE ...ATP SYNTHASE F(0) SECTOR SUBUNIT C / DICYCLOHEXYLCARBODIIMIDE-BINDING PROTEIN / F-TYPE ATPASE SUBUNIT C / F-ATPASE SUBUNIT C / LIPID-BINDING PROTEIN


Mass: 8259.064 Da / Num. of mol.: 1 / Fragment: MEMBRANE DOMAIN / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P68699

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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: MONOMERIC YIDC BOUND TO RIBOSOME NASCENT CHAIN COMPLEX(F0C)
Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jun 1, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
Image scansNum. digital images: 2000

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: DEFOCUS GROUP
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8 Å / Num. of particles: 58960 / Nominal pixel size: 1.035 Å
Details: ONLY THE MEMBRANE PART WAS MODELED SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2705. (DEPOSITION ID: 12685).
Symmetry type: POINT
RefinementHighest resolution: 8 Å
Refinement stepCycle: LAST / Highest resolution: 8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms552 0 0 0 552

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