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- PDB-6r7l: Ribosome-bound SecYEG translocon in a nanodisc -

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Basic information

Entry
Database: PDB / ID: 6r7l
TitleRibosome-bound SecYEG translocon in a nanodisc
Components
  • Protein translocase subunit SecY
  • SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
  • SecG
KeywordsMEMBRANE PROTEIN / monomeric translocon / nanodisc / insertion intermediate
Function / homology
Function and homology information


protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting ...protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / protein transmembrane transporter activity / protein secretion / protein targeting / intracellular protein transport / membrane => GO:0016020 / membrane / plasma membrane
Similarity search - Function
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 ...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
Similarity search - Domain/homology
Protein translocase subunit SecE / Protein translocase subunit SecE / Protein translocase subunit SecY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsKater, L. / Beckmann, R. / Kedrov, A.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationKE1879/3-1 Germany
German Research FoundationCRC 1208 Germany
European Research CouncilCRYOTRANSLATION
CitationJournal: EMBO Rep / Year: 2019
Title: Partially inserted nascent chain unzips the lateral gate of the Sec translocon.
Authors: Lukas Kater / Benedikt Frieg / Otto Berninghausen / Holger Gohlke / Roland Beckmann / Alexej Kedrov /
Abstract: The Sec translocon provides the lipid bilayer entry for ribosome-bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the ...The Sec translocon provides the lipid bilayer entry for ribosome-bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated role of the native environment in the translocon:ribosome assembly, structural information on the complex in the lipid membrane is scarce. Here, we present a cryo-electron microscopy-based structure of bacterial translocon SecYEG in lipid nanodiscs and elucidate an early intermediate state upon insertion of the FtsQ anchor domain. Insertion of the short nascent chain causes initial displacements within the lateral gate of the translocon, where α-helices 2b, 7, and 8 tilt within the membrane core to "unzip" the gate at the cytoplasmic side. Molecular dynamics simulations demonstrate that the conformational change is reversed in the absence of the ribosome, and suggest that the accessory α-helices of SecE subunit modulate the lateral gate conformation. Site-specific cross-linking validates that the FtsQ nascent chain passes the lateral gate upon insertion. The structure and the biochemical data suggest that the partially inserted nascent chain remains highly flexible until it acquires the transmembrane topology.
History
DepositionMar 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 25, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: entity / pdbx_unobs_or_zero_occ_atoms ...entity / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _struct_ref.db_code ..._entity.pdbx_description / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Dec 18, 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
G: SecG
E: SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
Y: Protein translocase subunit SecY


Theoretical massNumber of molelcules
Total (without water)61,3243
Polymers61,3243
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide SecG


Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#2: Protein SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE


Mass: 10880.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: A0A377BMD6, UniProt: P0AG96*PLUS
#3: Protein Protein translocase subunit SecY / SecY


Mass: 48553.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AGA2

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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: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 13098
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.53particle selection
2EM-Toolsimage acquisition
4Gctf1.06CTF correction
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 837184
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 112366 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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