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- PDB-5abb: Visualization of a polytopic membrane protein during SecY-mediate... -

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Basic information

Entry
Database: PDB / ID: 5abb
TitleVisualization of a polytopic membrane protein during SecY-mediated membrane insertion
Components
  • GREEN-LIGHT ABSORBING PROTEORHODOPSIN
  • PROTEIN TRANSLOCASE SUBUNIT SECE
  • PROTEIN TRANSLOCASE SUBUNIT SECY
KeywordsTRANSLATION / RIBOSOME / MEMBRANE PROTEIN / TRANSLOCON
Function / homology
Function and homology information


light-activated monoatomic ion channel activity / : / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein secretion / protein transmembrane transporter activity / photoreceptor activity ...light-activated monoatomic ion channel activity / : / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein secretion / protein transmembrane transporter activity / photoreceptor activity / phototransduction / protein targeting / proton transmembrane transport / intracellular protein transport / membrane / plasma membrane
Similarity search - Function
Proteorhodopsin / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family ...Proteorhodopsin / SecE subunit of protein translocation complex, bacterial-like / SecE superfamily / Protein translocase subunit SecY / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Bacterial rhodopsins signature 1. / Rhodopsin, retinal binding site / Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein
Similarity search - Domain/homology
Protein translocase subunit SecY / Protein translocase subunit SecE / Protein translocase subunit SecY / Green-light absorbing proteorhodopsin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å
AuthorsBischoff, L. / Wickles, S. / Berninghausen, O. / vanderSluis, E. / Beckmann, R.
CitationJournal: Nat Commun / Year: 2014
Title: Visualization of a polytopic membrane protein during SecY-mediated membrane insertion.
Authors: Lukas Bischoff / Stephan Wickles / Otto Berninghausen / Eli O van der Sluis / Roland Beckmann /
Abstract: The biogenesis of polytopic membrane proteins occurs co-translationally on ribosomes that are tightly bound to a membrane-embedded protein-conducting channel: the Sec-complex. The path that is ...The biogenesis of polytopic membrane proteins occurs co-translationally on ribosomes that are tightly bound to a membrane-embedded protein-conducting channel: the Sec-complex. The path that is followed by nascent proteins inside the ribosome and the Sec-complex is relatively well established; however, it is not clear what the fate of the N-terminal transmembrane domains (TMDs) of polytopic membrane proteins is when the C-terminal TMDs domains are not yet synthesized. Here, we present the sub-nanometer cryo-electron microscopy structure of an in vivo generated ribosome-SecY complex that carries a membrane insertion intermediate of proteorhodopsin (PR). The structure reveals a pre-opened Sec-complex and the first two TMDs of PR already outside the SecY complex directly in front of its proposed lateral gate. Thus, our structure is in agreement with positioning of N-terminal TMDs at the periphery of SecY, and in addition, it provides clues for the molecular mechanism underlying membrane protein topogenesis.
History
DepositionAug 5, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.2May 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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Structure visualization

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Assembly

Deposited unit
A: PROTEIN TRANSLOCASE SUBUNIT SECY
B: PROTEIN TRANSLOCASE SUBUNIT SECE
Z: GREEN-LIGHT ABSORBING PROTEORHODOPSIN


Theoretical massNumber of molelcules
Total (without water)68,8113
Polymers68,8113
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 PROTEIN TRANSLOCASE SUBUNIT SECY


Mass: 48553.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: B7MCR5, UniProt: P0AGA2*PLUS
#2: Protein PROTEIN TRANSLOCASE SUBUNIT SECE


Mass: 12623.296 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 12-127 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: B7MIW7
#3: Protein GREEN-LIGHT ABSORBING PROTEORHODOPSIN / GPR


Mass: 7634.684 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-83 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: Q9F7P4

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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: TnaC stalled E.coli ribosome in complex with SecYE / Type: RIBOSOME
Buffer solutionName: 20 MM TRIS 150 MM NH4CL 10 MM MGCL2 0.05%DDM 125 MM SUCROSE
pH: 7.5
Details: 20 MM TRIS 150 MM NH4CL 10 MM MGCL2 0.05%DDM 125 MM SUCROSE
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: May 21, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 148721 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: REAL / Resolution: 8 Å / Num. of particles: 47471 / Symmetry type: POINT
RefinementHighest resolution: 8 Å
Refinement stepCycle: LAST / Highest resolution: 8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 0 0 2512

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