6C26

The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex

  • Classification: TRANSFERASE
  • Organism(s): Saccharomyces cerevisiae S288C
  • Mutation(s): No 

  • Deposited: 2018-01-06 Released: 2018-01-31 
  • Deposition Author(s): Bai, L., Li, H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

The atomic structure of a eukaryotic oligosaccharyltransferase complex.

Bai, L., Wang, T., Zhao, G., Kovach, A., Li, H.

(2018) Nature 555: 328-333

  • DOI: 10.1038/nature25755
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • N-glycosylation is a ubiquitous modification of eukaryotic secretory and membrane-bound proteins; about 90% of glycoproteins are N-glycosylated. The reaction is catalysed by an eight-protein oligosaccharyltransferase (OST) complex that is embedded in ...

    N-glycosylation is a ubiquitous modification of eukaryotic secretory and membrane-bound proteins; about 90% of glycoproteins are N-glycosylated. The reaction is catalysed by an eight-protein oligosaccharyltransferase (OST) complex that is embedded in the endoplasmic reticulum membrane. Our understanding of eukaryotic protein N-glycosylation has been limited owing to the lack of high-resolution structures. Here we report a 3.5 Å resolution cryo-electron microscopy structure of the Saccharomyces cerevisiae OST complex, revealing the structures of subunits Ost1-Ost5, Stt3, Wbp1 and Swp1. We found that seven phospholipids mediate many of the inter-subunit interactions, and an Stt3 N-glycan mediates interactions with Wbp1 and Swp1 in the lumen. Ost3 was found to mediate the OST-Sec61 translocon interface, funnelling the acceptor peptide towards the OST catalytic site as the nascent peptide emerges from the translocon. The structure provides insights into co-translational protein N-glycosylation, and may facilitate the development of small-molecule inhibitors that target this process.

    Organizational Affiliation: 

    Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A718Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STT3, YGL022W
EC: 2.4.99.18
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oligosaccharyltransferases (OST)		Protein: 
Eukaryotic oligosaccharyltransferase Complex
Find proteins for P39007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P39007
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 11476Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST1, NLT1, YJL002C, J1404
EC: 2.4.99.18
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oligosaccharyltransferases (OST)		Protein: 
Eukaryotic oligosaccharyltransferase Complex
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: 3
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5586Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST5, YGL226C-A, YGL226BC
EC: 2.4.99.18
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oligosaccharyltransferases (OST)		Protein: 
Eukaryotic oligosaccharyltransferase Complex
Find proteins for Q92316 (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 OST4436Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST4, YDL232W
EC: 2.4.99.18
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oligosaccharyltransferases (OST)		Protein: 
Eukaryotic oligosaccharyltransferase Complex
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 OST22130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST2, YOR103C, YOR3211C
EC: 2.4.99.18
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oligosaccharyltransferases (OST)		Protein: 
Eukaryotic oligosaccharyltransferase Complex
Find proteins for P46964 (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 33350Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST3, YOR085W, YOR3124W
EC: 2.4.99.18
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oligosaccharyltransferases (OST)		Protein: 
Eukaryotic oligosaccharyltransferase Complex
Find proteins for P48439 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P48439
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  • Reference Sequence

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1C286Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWP1, YMR149W, YM9375.19
EC: 2.4.99.18
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oligosaccharyltransferases (OST)		Protein: 
Eukaryotic oligosaccharyltransferase Complex
Find proteins for Q02795 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1B430Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: WBP1, YEL002C
EC: 2.4.99.18
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Oligosaccharyltransferases (OST)		Protein: 
Eukaryotic oligosaccharyltransferase Complex
Find proteins for P33767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33767 
Go to UniProtKB:  P33767
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  • Reference Sequence
Oligosaccharides
Entity ID: 9
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-2)-[beta-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
D
7 N-Glycosylation
Entity ID: 10
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
E
3 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EGY
Query on EGY
Download CCD File 
1, 3, 4, A, C
(4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)methyl]-3,5,8-trioxa-4lambda~5~-phosphadocosan-1-aminium
C33 H67 N O8 P
GGHWXDCJHDYMKO-WJOKGBTCSA-O		 Ligand Interaction
NAG
Query on NAG
Download CCD File 
B
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: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-06 
  • Released Date: 2018-01-31 
    • Deposition Author(s): Bai, L., Li, H.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM111742

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Author supporting evidence
  • Version 1.2: 2018-03-07
    Changes: Database references
  • Version 1.3: 2018-03-28
    Changes: Data collection, Database references
  • Version 1.4: 2019-12-18
    Changes: Author supporting evidence, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary