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- EMDB-4257: Additional yeast OST cryoEM maps from focused 3D refinements -

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Basic information

Entry
Database: EMDB / ID: EMD-4257
TitleAdditional yeast OST cryoEM maps from focused 3D refinements
Map dataLuminal part of OST, Post-processed, masked map, "Map 2"
Sample
  • Complex: yeast OST
Biological speciesSaccharomyces (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWild R / Kowal J / Eyring J / Ngwa EM / Aebi M / Locher KP
CitationJournal: Science / Year: 2018
Title: Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.
Authors: Rebekka Wild / Julia Kowal / Jillianne Eyring / Elsy M Ngwa / Markus Aebi / Kaspar P Locher /
Abstract: Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to ...Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to glycosylation sites of secretory proteins. Here we describe the atomic structure of yeast OST determined by cryo-electron microscopy, revealing a conserved subunit arrangement. The active site of the catalytic STT3 subunit points away from the center of the complex, allowing unhindered access to substrates. The dolichol-pyrophosphate moiety binds to a lipid-exposed groove of STT3, whereas two noncatalytic subunits and an ordered N-glycan form a membrane-proximal pocket for the oligosaccharide. The acceptor polypeptide site faces an oxidoreductase domain in stand-alone OST complexes or is immediately adjacent to the translocon, suggesting how eukaryotic OSTs efficiently glycosylate a large number of polypeptides before their folding.
History
DepositionJan 9, 2018-
Header (metadata) releaseJan 17, 2018-
Map releaseJan 17, 2018-
UpdateFeb 21, 2018-
Current statusFeb 21, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4257.png

Downloads & links

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Map

FileDownload / File: emd_4257.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLuminal part of OST, Post-processed, masked map, "Map 2"
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 319.5 Å		1.07 Å/pix.
x 300 pix.
= 319.5 Å		1.07 Å/pix.
x 300 pix.
= 319.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.16648522 - 0.25800568
Average (Standard dev.)0.00016168084 (±0.0045478283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 319.50003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z319.500319.500319.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1660.2580.000

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Supplemental data

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Additional map: Transmembrane region of OST, Post-processed, masked map, "Map 3"

Fileemd_4257_additional_1.map
AnnotationTransmembrane region of OST, Post-processed, masked map, "Map 3"
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: OST1 region of OST, Post-processed, masked map, "Map 5"

Fileemd_4257_additional_2.map
AnnotationOST1 region of OST, Post-processed, masked map, "Map 5"
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: SWP1 region of OST, Post-processed, masked map, "Map 4"

Fileemd_4257_additional_3.map
AnnotationSWP1 region of OST, Post-processed, masked map, "Map 4"
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : yeast OST

EntireName: yeast OST
Components
  • Complex: yeast OST

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Supramolecule #1: yeast OST

SupramoleculeName: yeast OST / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces (fungus)

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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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 110091
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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