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- EMDB-4743: Ribosome-bound SecYEG translocon in a nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-4743
TitleRibosome-bound SecYEG translocon in a nanodisc
Map data
SampleStalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
  • SecG
  • SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
  • Protein translocase subunit SecY
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 / SRP-dependent cotranslational protein targeting to membrane, translocation / intracellular protein transmembrane transport / signal sequence binding / protein transmembrane transporter activity / intracellular protein transport / integral component of plasma membrane / integral component of membrane / plasma membrane
SecY domain superfamily / Protein secY signature 2. / Protein secY signature 1. / SecY translocase / SecY conserved site / Protein translocase subunit SecY / SecY/SEC61-alpha family
un:a0a0t5xnm1: / Protein translocase subunit SecY
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsKater L / Beckmann R / Kedrov A
Funding support Germany, 3 items
OrganizationGrant numberCountry
German Research FoundationKE1879/3-1 Germany
European Research CouncilCRYOTRANSLATION
German Research FoundationCRC 1208 Germany
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.
Validation ReportPDB-ID: 6r7l

SummaryFull reportAbout validation report
History
DepositionMar 29, 2019-
Header (metadata) releaseAug 7, 2019-
Map releaseAug 7, 2019-
UpdateAug 14, 2019-
Current statusAug 14, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6r7l
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6r7l
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4743.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.17 Å/pix.
x 80 pix.
= 173.44 Å
2.17 Å/pix.
x 80 pix.
= 173.44 Å
2.17 Å/pix.
x 80 pix.
= 173.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.168 Å
Density
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.2704685 - 0.542913
Average (Standard dev.)-0.0021569747 (±0.019495174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 173.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.1682.1682.168
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z173.440173.440173.440
α/β/γ90.00090.00090.000
start NX/NY/NZ-15-9-23
NX/NY/NZ635180
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.2700.543-0.002

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Supplemental data

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Sample components

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Entire Stalled E. coli ribosome nascent chain complex (RNC) bound to the...

EntireName: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
Number of components: 4

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Component #1: protein, Stalled E. coli ribosome nascent chain complex (RNC) bou...

ProteinName: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli)

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Component #2: protein, SecG

ProteinName: SecG / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.890321 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #3: protein, SecE,Protein translocase subunit SecE,Protein translocas...

ProteinName: SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.880122 kDa
SourceSpecies: Escherichia coli (E. coli)

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Component #4: protein, Protein translocase subunit SecY

ProteinName: Protein translocase subunit SecY / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.553375 kDa
SourceSpecies: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.5 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 13098

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 112366
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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