6EZN

Cryo-EM structure of the yeast oligosaccharyltransferase (OST) complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.

Wild, R., Kowal, J., Eyring, J., Ngwa, E.M., Aebi, M., Locher, K.P.

(2018) Science 359: 545-550

  • DOI: 10.1126/science.aar5140
  • Structures With Same Primary Citation

  • PubMed 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 glycosylation sites of secretory proteins. Here we describe ...

    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.

    Organizational Affiliation: 

    Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland. markus.aebi@micro.biol.ethz.ch locher@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1A476Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST1, NLT1, YJL002C, J1404
EC: 2.4.99.18
Find proteins for P41543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P41543
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2B130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST2, YOR103C, YOR3211C
EC: 2.4.99.18
Find proteins for P46964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3C350Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST3, YOR085W, YOR3124W
EC: 2.4.99.18
Find proteins for P48439 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4D36Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST4, YDL232W
EC: 2.4.99.18
Find proteins for Q99380 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5E86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST5, YGL226C-A, YGL226BC
EC: 2.4.99.18
Find proteins for Q92316 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3F718Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STT3, YGL022W
EC: 2.4.99.18
Find proteins for P39007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1G430Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: WBP1, YEL002C
EC: 2.4.99.18
Find proteins for P33767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1H286Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWP1, YMR149W, YM9375.19
EC: 2.4.99.18
Find proteins for Q02795 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
Oligosaccharides
Entity ID: 9
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
3 N-Glycosylation
Entity ID: 10
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, L
2 N-Glycosylation
Entity ID: 11
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
8 N-Glycosylation
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPL
Query on CPL
Download CCD File 
A, E, F, H
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N		 Ligand Interaction
PTY
Query on PTY
Download CCD File 
F
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N		 Ligand Interaction
NAG
Query on NAG
Download CCD File 
G
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandSNF Synergia Transglyco: CRSII3_147632
Swiss National Science FoundationSwitzerlandSNF Sinergia GlycoSTART: CRSII5_173709/1

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2019-12-11
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary