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

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Basic information

Entry
Database: EMDB / ID: EMD-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
Sample
  • Complex: 80S ribosome from STT3A(-/-) HEK cells bound to the endoplasmic reticulum protein transloconEukaryotic ribosome
    • Complex: OST-free protein translocon complexes of the endoplasmic reticulum
Function / homology
Function and homology information


oligosaccharyltransferase III complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / oligosaccharyltransferase complex / pronephric nephron development / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / cotranslational protein targeting to membrane ...oligosaccharyltransferase III complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / endoplasmic reticulum Sec complex / oligosaccharyltransferase complex / pronephric nephron development / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / post-translational protein targeting to membrane, translocation / protein glycosylation / protein transmembrane transporter activity / rough endoplasmic reticulum / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-translational protein modification / cytosolic ribosome / phospholipid binding / ribosome binding / ribosome biogenesis / 5S rRNA binding / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / endoplasmic reticulum membrane / nucleolus / endoplasmic reticulum / RNA binding / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Oligosaccharyltransferase complex subunit OSTC / Ribophorin I / Ribophorin I / Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / : / STT3/PglB/AglB core domain / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal ...Oligosaccharyltransferase complex subunit OSTC / Ribophorin I / Ribophorin I / Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / : / STT3/PglB/AglB core domain / : / Oligosaccharyl transferase, STT3 subunit / Oligosaccharyl transferase STT3, N-terminal / Protein transport Sec61-beta/Sbh / Protein transport protein SecG/Sec61-beta/Sbh / Sec61beta family / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / 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 / 60S acidic ribosomal protein P0 / Ribosomal protein L6, N-terminal / Ribosomal protein L6, N-terminal domain / : / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L29e / Ribosomal protein L41 / Ribosomal protein L41 / Ribosomal L29e protein family / Ribosomal Protein L6, KOW domain / 60S ribosomal protein L6E / Ribosomal protein L44e signature. / Ribosomal protein L27e signature. / Ribosomal protein L10e signature. / Ribosomal protein L6e / Ribosomal protein L24e signature. / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L34e signature. / Ribosomal protein L6e signature. / Ribosomal protein L36e signature. / Ribosomal protein L39e signature. / Ribosomal protein L6, conserved site-2 / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / Ribosomal protein L35Ae signature. / Ribosomal protein L31e signature. / Ribosomal protein L14e domain / Ribosomal protein L14 / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L32e, conserved site / Ribosomal protein L32e signature. / Ribosomal protein L14 / Ribosomal protein L6 signature 2. / Ribosomal protein L14, KOW motif / Ribosomal protein L1e signature. / Ribosomal protein L15e signature. / Ribosomal protein L21e signature. / Ribosomal protein L7, eukaryotic/archaeal / Ribosomal protein L7/L30 / Ribosomal protein L37e signature. / Ribosomal protein L32e / Ribosomal protein L32e superfamily / Ribosomal protein L32 / Ribosomal_L32e / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / Ribosomal protein L30 signature. / Ribosomal protein L5 signature. / Ribosomal protein L29 signature. / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L6 / Ribosomal protein L15 signature. / Ribosomal protein L14 signature. / Ribosomal protein L22 signature. / Ribosomal protein L24 signature. / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L3 signature. / Translation protein SH3-like domain superfamily / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
60S ribosomal protein L41 / Large ribosomal subunit protein uL16 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 ...60S ribosomal protein L41 / Large ribosomal subunit protein uL16 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1 / Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A / Large ribosomal subunit protein eL24 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein eL33 / Large ribosomal subunit protein eL31 / Large ribosomal subunit protein eL21 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein eL8 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein eL39 / Large ribosomal subunit protein eL42 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein uL14 / 60S ribosomal protein L6 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein eL29 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein eL36 / Large ribosomal subunit protein uL5 / Ribosomal protein L32 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL27 / 60S acidic ribosomal protein P0 / Large ribosomal subunit protein eL28 / Large ribosomal subunit protein eL34 / Protein transport protein Sec61 subunit alpha isoform 1 / Protein transport protein Sec61 subunit gamma / Protein transport protein Sec61 subunit beta / Oligosaccharyltransferase complex subunit OSTC / Large ribosomal subunit protein eL14 / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
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.
History
DepositionFeb 22, 2018-
Header (metadata) releaseMar 21, 2018-
Map releaseMar 21, 2018-
UpdateNov 28, 2018-
Current statusNov 28, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • 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

emd_4310.png

Downloads & links

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Map

FileDownload / File: emd_4310.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of OST-free ribosome-translocon complexes from STT3A(-/-) HEK cells
Voxel sizeX=Y=Z: 5.24 Å
Density
Contour LevelBy AUTHOR: 2. / Movie #1: 2
Minimum - Maximum-10.105926999999999 - 11.825587000000001
Average (Standard dev.)-0.000000004395392 (±0.99999964)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 576.39996 Å
α=β=γ: 90.0 °

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
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 transloconEukaryotic ribosome
Components
  • Complex: 80S ribosome from STT3A(-/-) HEK cells bound to the endoplasmic reticulum protein transloconEukaryotic ribosome
    • Complex: OST-free protein translocon complexes of the endoplasmic reticulum

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Supramolecule #1: 80S ribosome from STT3A(-/-) HEK cells bound to the endoplasmic r...

SupramoleculeName: 80S ribosome from STT3A(-/-) HEK cells bound to the endoplasmic reticulum protein translocon
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: OST-free protein translocon complexes of the endoplasmic reticulum

SupramoleculeName: OST-free protein translocon complexes of the endoplasmic reticulum
type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 77 / Number images used: 793 / Software - Name: PyTom
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 525

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