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


This is version 2.1 of the entry. See complete history


Literature

Molecular basis for glycan recognition and reaction priming of eukaryotic oligosaccharyltransferase.

Ramirez, A.S.de Capitani, M.Pesciullesi, G.Kowal, J.Bloch, J.S.Irobalieva, R.N.Reymond, J.L.Aebi, M.Locher, K.P.

(2022) Nat Commun 13: 7296-7296

  • DOI: https://doi.org/10.1038/s41467-022-35067-x
  • Primary Citation of Related Structures:  
    6EZN, 8AGB, 8AGC, 8AGE

  • PubMed Abstract: 

    Oligosaccharyltransferase (OST) is the central enzyme of N-linked protein glycosylation. It catalyzes the transfer of a pre-assembled glycan, GlcNAc 2 Man 9 Glc 3 , from a dolichyl-pyrophosphate donor to acceptor sites in secretory proteins in the lumen of the endoplasmic reticulum. Precise recognition of the fully assembled glycan by OST is essential for the subsequent quality control steps of glycoprotein biosynthesis. However, the molecular basis of the OST-donor glycan interaction is unknown. Here we present cryo-EM structures of S. cerevisiae OST in distinct functional states. Our findings reveal that the terminal glucoses (Glc 3 ) of a chemo-enzymatically generated donor glycan analog bind to a pocket formed by the non-catalytic subunits WBP1 and OST2. We further find that binding either donor or acceptor substrate leads to distinct primed states of OST, where subsequent binding of the other substrate triggers conformational changes required for catalysis. This alternate priming allows OST to efficiently process closely spaced N-glycosylation sites.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1476Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P41543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41543 
Go to UniProtKB:  P41543
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41543
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2130Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P46964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46964 
Go to UniProtKB:  P46964
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46964
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3350Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P48439 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P48439 
Go to UniProtKB:  P48439
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48439
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST436Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for Q99380 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99380 
Go to UniProtKB:  Q99380
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99380
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST586Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for Q92316 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q92316 
Go to UniProtKB:  Q92316
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92316
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3718Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P39007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39007 
Go to UniProtKB:  P39007
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39007
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1430Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P33767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P33767 
Go to UniProtKB:  P33767
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33767
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1286Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for Q02795 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02795 
Go to UniProtKB:  Q02795
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02795
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, L
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83582BK
GlyCosmos:  G83582BK
GlyGen:  G83582BK
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTPHENIX1.11

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • 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
  • Version 2.1: 2022-12-07
    Changes: Database references, Derived calculations, Structure summary