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- EMDB-4310: Subtomogram average of OST-free ribosome-translocon complexes fro... -

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Entry
Database: EMDB / ID: 4310
TitleSubtomogram average of OST-free ribosome-translocon complexes from STT3A(-/-) HEK cells
Map dataSubtomogram average of OST-free ribosome-translocon complexes from STT3A(-/-) HEK cells
Sample80S ribosome from STT3A(-/-) HEK cells bound to the endoplasmic reticulum protein translocon
Function/homologyRibophorin I / |Ribophorin I / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / dolichyl-diphosphooligosaccharide---protein glycotransferase / Oligosaccharyl transferase complex, subunit OST3/OST6 / pronephric nephron development / XBP1(S) activates chaperone genes / OST3 / OST6 family, transporter family / Protein transport Sec61-beta/Sbh / membrane docking ...Ribophorin I / |Ribophorin I / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / dolichyl-diphosphooligosaccharide---protein glycotransferase / Oligosaccharyl transferase complex, subunit OST3/OST6 / pronephric nephron development / XBP1(S) activates chaperone genes / OST3 / OST6 family, transporter family / Protein transport Sec61-beta/Sbh / membrane docking / Sec61 translocon complex / oligosaccharyl transferase activity / Translocon Sec61/SecY, plug domain / oligosaccharyltransferase complex / Oligosaccharyl transferase, STT3 subunit / posttranslational protein targeting to membrane, translocation / optic nerve development / endoplasmic reticulum Sec complex / Protein transport protein SecG/Sec61-beta/Sbh / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Oligosaccharyl transferase STT3 subunit / Plug domain of Sec61p / Sec61beta family / Protein secE/sec61-gamma signature. / Protein translocase complex, SecE/Sec61-gamma subunit / Ribosomal protein L6, N-terminal / negative regulation of protein neddylation / Protein secY signature 2. / protein targeting to ER / Protein secY signature 1. / protein-DNA complex disassembly / positive regulation of signal transduction by p53 class mediator / Preprotein translocase subunit SecE / SecY domain superfamily / SecY conserved site / SecY/SEC61-alpha family / exit from mitosis / Ribosomal protein L6, N-terminal domain / SecE/Sec61-gamma subunits of protein translocation complex / ubiquitin ligase inhibitor activity / Ribosomal protein L28e / SRP-dependent cotranslational protein targeting to membrane, translocation / Ribosomal L28e/Mak16 / ARF guanyl-nucleotide exchange factor activity / P-P-bond-hydrolysis-driven protein transmembrane transporter activity / SecY translocase / 60S acidic ribosomal protein P0 / retrograde protein transport, ER to cytosol / retinal ganglion cell axon guidance / Ribosomal L28e protein family / negative regulation of ubiquitin-dependent protein catabolic process / protein N-linked glycosylation via asparagine / Ribosomal protein L2, archaeal-type / Ribosomal protein L23 / Ribosomal protein L41 / TRASH domain / Ribosomal protein L27e signature. / Ribosomal protein L27e, conserved site / Ribosomal protein L6e signature. / Ribosomal protein L29e / integral component of endoplasmic reticulum membrane / Ribosomal protein L34e signature. / Ribosomal protein L34e, conserved site / Ribosomal protein L35Ae, conserved site / Ribosomal protein L35Ae signature. / Ribosomal protein L23/L25, N-terminal / Ribosomal protein L36e signature. / Ribosomal protein L27e / Ribosomal protein L5 eukaryotic/L18 archaeal, C-terminal / 60S ribosomal protein L6E / Ribosomal protein L7, eukaryotic / Ribosomal protein L34Ae / Ribosomal protein L30, N-terminal / Ribosomal protein L7A/L8 / Ribosomal protein L36e / 60S ribosomal protein L4, C-terminal domain / Ribosomal protein L35A / Ribosomal protein L14e domain / Ribosomal protein L41 / epidermal growth factor binding / Ribosomal protein L24e signature. / Ribosomal protein L24e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L10e, conserved site / Ribosomal protein L34e / Ribosomal protein L44e signature. / Ribosomal protein L10e / Ribosomal protein L15e signature. / Ribosomal protein L44e / Ribosomal protein L15e, conserved site / Ribosomal protein L37ae / Ribosomal protein L31e, conserved site / Ribosomal protein L31e signature. / Ribosomal protein L32e signature. / Ribosomal protein L32e, conserved site / Ribosomal protein L23, N-terminal domain / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L5 eukaryotic/L18 archaeal
Function and homology information
SourceHomo sapiens / human /
Methodsubtomogram averaging, at 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.
Copyright: 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.
DateDeposition: Feb 22, 2018 / Header (metadata) release: Mar 21, 2018 / Map release: Mar 21, 2018 / Last update: Mar 21, 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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3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_4310.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 package.

Voxel sizeX=Y=Z: 5.24 Å
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-10.105926999999999 - 11.825587000000001
Average (Standard dev.)-0.000000004395392 (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-10.10611.826-0.000

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Supplemental data

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Sample components

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Entire 80S ribosome from STT3A(-/-) HEK cells bound to the endoplasmic r...

EntireName: 80S ribosome from STT3A(-/-) HEK cells bound to the endoplasmic reticulum protein translocon
Number of components: 2

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Component #1: protein, 80S ribosome from STT3A(-/-) HEK cells bound to the endo...

ProteinName: 80S ribosome from STT3A(-/-) HEK cells bound to the endoplasmic reticulum protein translocon
Recombinant expression: No
SourceSpecies: Homo sapiens / human /

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Component #2: protein, OST-free protein translocon complexes of the endoplasmic...

ProteinName: OST-free protein translocon complexes of the endoplasmic reticulum
Recombinant expression: No
SourceSpecies: Homo sapiens / human /

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Experimental details

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Sample preparation

Specimen stateparticle
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
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.5 CUT-OFF

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