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- EMDB-4306: Subtomogram average of unsorted ribosome-translocon complexes fro... -

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Entry
Database: EMDB / ID: 4306
TitleSubtomogram average of unsorted ribosome-translocon complexes from STT3B(-/-) HEK cells
Map dataSubtomogram average of unsorted ribosome-translocon complexes from STT3B(-/-) HEK cells
Sample80S ribosome from STT3B(-/-) HEK cells bound to the endoplasmic reticulum protein translocon
  • Protein translocon complex of the endoplasmic reticulum
Function / homologyRibosomal protein L30, central domain, archaeal type / Ribosomal protein L31e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Translocon Sec61/SecY, plug domain / Ribosomal protein L3, conserved site / Ribosomal protein L14P, conserved site ...Ribosomal protein L30, central domain, archaeal type / Ribosomal protein L31e, conserved site / Ribosomal protein L27e, conserved site / Ribosomal protein L32e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L37e, conserved site / Ribosomal protein L7Ae/L8/Nhp2 family / Translocon Sec61/SecY, plug domain / Ribosomal protein L3, conserved site / Ribosomal protein L14P, conserved site / Ribosomal protein L23 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L39e, conserved site / Ribosomal protein L21e, conserved site / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L15e, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L18e/L15P / Oligosaccharyl transferase complex, subunit OST3/OST6 / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2, C-terminal / Ribosomal protein L2, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L10e, conserved site / in:ipr022943: / Nucleic acid-binding, OB-fold / Ribosomal protein L7, eukaryotic / Ribophorin I / Ribosomal protein L41 / Protein translocase SEC61 complex, gamma subunit / Ribosomal protein L34Ae / Translation protein SH3-like domain superfamily / Translation protein, beta-barrel domain superfamily / TRASH domain / Ribosomal protein L37ae/L37e / Zinc-binding ribosomal protein / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L29, conserved site / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein L30, N-terminal / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L25/L23 / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L10e/L16 / Protein transport protein SecG/Sec61-beta/Sbh / Ribosomal protein L30, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / KOW / Ribosomal protein L14p/L23e / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L21 superfamily / Ribosomal protein L36e domain superfamily / Ribosomal protein L7A/L8 superfamily / Ribosomal protein L34Ae superfamily / Ribosomal protein L24e/L24 superfamily / Ribosomal protein L27e superfamily / Ribosomal protein L35A superfamily / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L16p/L10e / Ribosomal protein L14 superfamily / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L11, RNA binding domain / Ribosomal protein L30p/L7e / SecY translocase / Ribosomal protein L6 / Ribosomal protein L10 / KOW motif / Ribosomal protein L4/L1 family / SecE/Sec61-gamma subunits of protein translocation complex / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / SecY domain superfamily / 50S ribosomal protein L30e-like / Protein translocase SecE domain superfamily / Ribosomal protein L24e, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L31e domain superfamily / Ribosomal protein L39e domain superfamily / Ribosomal protein L2, archaeal-type / Ribosomal protein L15e core domain superfamily / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L4, C-terminal domain / Ribosomal L28e/Mak16 / SecY conserved site / Ribosomal protein L6, alpha-beta domain superfamily / 60S acidic ribosomal protein P0 / Protein transport Sec61-beta/Sbh / Ribosomal protein L15 / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / Ribosomal protein L7, eukaryotic/archaeal
Function and homology information
SourceHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / 30 Å resolution
AuthorsPfeffer S / Foerster F
CitationJournal: Science / Year: 2018
Title: Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum.
Authors: Katharina Braunger / Stefan Pfeffer / Shiteshu Shrimal / Reid Gilmore / Otto Berninghausen / Elisabet C Mandon / Thomas Becker / Friedrich Förster / Roland Beckmann
Abstract: Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and ...Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and oligosaccharyltransferase (OST). Here we used different cryo-electron microscopy approaches to determine structures of native and solubilized ribosome-Sec61-OST complexes. A molecular model for the catalytic OST subunit STT3A (staurosporine and temperature sensitive 3A) revealed how it is integrated into the OST and how STT3-paralog specificity for translocon-associated OST is achieved. The OST subunit DC2 was placed at the interface between Sec61 and STT3A, where it acts as a versatile module for recruitment of STT3A-containing OST to the ribosome-Sec61 complex. This detailed structural view on the molecular architecture of the cotranslational machinery for N-glycosylation provides the basis for a mechanistic understanding of glycoprotein biogenesis at the endoplasmic reticulum.
DateDeposition: Feb 22, 2018 / Header (metadata) release: Mar 21, 2018 / Map release: Mar 21, 2018 / Last update: Apr 25, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4306.map.gz (map file in CCP4 format, 5325 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
110 pix
5.24 Å/pix.
= 576.4 Å
110 pix
5.24 Å/pix.
= 576.4 Å
110 pix
5.24 Å/pix.
= 576.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.24 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-10.976915 - 12.630468
Average (Standard dev.)-0.000000004982974 (0.99999964)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions110110110
Origin000
Limit109109109
Spacing110110110
CellA=B=C: 576.39996 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.245.245.24
M x/y/z110110110
origin x/y/z0.0000.0000.000
length x/y/z576.400576.400576.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS110110110
D min/max/mean-10.97712.630-0.000

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Supplemental data

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Sample components

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Entire 80S ribosome from STT3B(-/-) HEK cells bound to the endoplasmic r...

EntireName: 80S ribosome from STT3B(-/-) HEK cells bound to the endoplasmic reticulum protein translocon
Number of components: 2

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Component #1: protein, 80S ribosome from STT3B(-/-) HEK cells bound to the endo...

ProteinName: 80S ribosome from STT3B(-/-) HEK cells bound to the endoplasmic reticulum protein translocon
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Component #2: protein, Protein translocon complex of the endoplasmic reticulum

ProteinName: Protein translocon complex of the endoplasmic reticulum
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE-PROPANE MIXTURE

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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: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER / Tilt Angle: -60 - 60 deg.
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.5 CUT-OFF

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