6C26

The Cryo-EM structure of a eukaryotic oligosaccharyl transferase complex


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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
  • Primary Citation of Related Structures:  
    6C26

  • 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 the endoplasmic reticulum membrane ...

    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 LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A718Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STT3YGL022W
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P39007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP39007
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1B [auth 1]476Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST1NLT1YJL002CJ1404
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P41543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5C [auth 5]86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST5YGL226C-AYGL226BC
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for Q92316 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4D [auth 4]36Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST4YDL232W
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for Q99380 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2E [auth 2]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST2YOR103CYOR3211C
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P46964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3F [auth 3]350Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST3YOR085WYOR3124W
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1G [auth C]286Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWP1YMR149WYM9375.19
EC: 2.4.99.18
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1H [auth B]430Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: WBP1YEL002C
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P33767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Oligosaccharides

Help

Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseI [auth D]7N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G50777HT
GlyCosmos:  G50777HT
GlyGen:  G50777HT
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth E]3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EGY
Query on EGY

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A],
M [auth A],
N [auth 1],
O [auth 1],
K [auth A],
L [auth A],
M [auth A],
N [auth 1],
O [auth 1],
P [auth 4],
Q [auth 3],
R [auth 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 Ideal Coordinates CCD File 
S [auth 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




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  (Full details and data files)

  • 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