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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 dataSecYEG:Nanodisc portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement.
Sample
  • Complex: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
    • Protein or peptide: SecG
    • Protein or peptide: SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
    • Protein or peptide: 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 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.
History
DepositionMar 29, 2019-
Header (metadata) releaseAug 7, 2019-
Map releaseAug 7, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing 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
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  • 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
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6r7l
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4743.png

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)
AnnotationSecYEG:Nanodisc portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement.
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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Additional map: Large ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex...

Fileemd_4743_additional_1.map
AnnotationLarge ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement. This map includes the tRNA, nascent chain, SecYEG and nanodisc. Filtered according to local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Large ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex...

Fileemd_4743_additional_2.map
AnnotationLarge ribosomal subunit portion of the RNC:SecYEG:Nanodisc complex after multi-body refinement. This map includes the tRNA, nascent chain, SecYEG and nanodisc. Filtered according to local resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Components
  • Complex: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
    • Protein or peptide: SecG
    • Protein or peptide: SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
    • Protein or peptide: Protein translocase subunit SecY

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Supramolecule #1: Stalled E. coli ribosome nascent chain complex (RNC) bound to the...

SupramoleculeName: Stalled E. coli ribosome nascent chain complex (RNC) bound to the translocon SecYEG in a nanodisc
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: SecG

MacromoleculeName: SecG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.890321 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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Macromolecule #2: SecE,Protein translocase subunit SecE,Protein translocase subunit...

MacromoleculeName: SecE,Protein translocase subunit SecE,Protein translocase subunit SecE,Protein translocase subunit SecE
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 10.880122 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)LLTTKGKAT VAFAREARTE VRKVIWPTRQ ETLHTTLIVA AVTAVM SLI LWGLDGILVR LVSFITGLRF

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Macromolecule #3: Protein translocase subunit SecY

MacromoleculeName: Protein translocase subunit SecY / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 48.553375 KDa
SequenceString: MAKQPGLDFQ SAKGGLGELK RRLLFVIGAL IVFRIGSFIP IPGIDAAVLA KLLEQQRGTI IEMFNMFSGG ALSRASIFAL GIMPYISAS IIIQLLTVVH PTLAEIKKEG ESGRRKISQY TRYGTLVLAI FQSIGIATGL PNMPGMQGLV INPGFAFYFT A VVSLVTGT ...String:
MAKQPGLDFQ SAKGGLGELK RRLLFVIGAL IVFRIGSFIP IPGIDAAVLA KLLEQQRGTI IEMFNMFSGG ALSRASIFAL GIMPYISAS IIIQLLTVVH PTLAEIKKEG ESGRRKISQY TRYGTLVLAI FQSIGIATGL PNMPGMQGLV INPGFAFYFT A VVSLVTGT MFLMWLGEQI TERGIGNGIS IIIFAGIVAG LPPAIAHTIE QARQGDLHFL VLLLVAVLVF AVTFFVVFVE RG QRRIVVN YAKRQQGRRV YAAQSTHLPL KVNMAGVIPA IFASSIILFP ATIASWFGGG TGWNWLTTIS LYLQPGQPLY VLL YASAII FFCFFYTALV FNPRETADNL KKSGAFVPGI RPGEQTAKYI DKVMTRLTLV GALYITFICL IPEFMRDAMK VPFY FGGTS LLIVVVVIMD FMAQVQTLMM SSQYESALKK ANLKGYGR

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 13098 / Average electron dose: 2.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 837184
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 112366
FSC plot (resolution estimation)

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