8AGC

Structure of yeast oligosaccharylransferase complex with lipid-linked oligosaccharide and non-acceptor peptide bound


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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

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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycotransferase718Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: STT3GI527_G0002399
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt
Find proteins for P39007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P39007
Entity Groups  
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UniProt GroupP39007
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P39007-1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
OST4 isoform 165Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OST4GI527_G0000704
Membrane Entity: Yes 
UniProt
Find proteins for Q99380 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ99380
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST586Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OST5YGL226C-AYGL226BC
Membrane Entity: Yes 
UniProt
Find proteins for Q92316 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ92316
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2130Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OST2GI527_G0005476
Membrane Entity: Yes 
UniProt
Find proteins for P46964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP46964
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1476Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OST1GI527_G0003255
Membrane Entity: Yes 
UniProt
Find proteins for P41543 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP41543
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P41543-1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2283Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SWP1GI527_G0004591
Membrane Entity: Yes 
UniProt
Find proteins for Q02795 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1430Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: WBP1GI527_G0001785
Membrane Entity: Yes 
UniProt
Find proteins for P33767 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP33767
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P33767-1
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
OST3 isoform 1350Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: OST3GI527_G0005459
Membrane Entity: Yes 
UniProt
Find proteins for P48439 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP48439
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDEI [auth P]7Saccharomyces cerevisiaeMutation(s): 0 
Sequence Annotations
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Oligosaccharides

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Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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-glucopyranoseJ [auth I]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46836GH
GlyCosmos:  G46836GH
GlyGen:  G46836GH
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J],
L [auth K]
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-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-alpha-D-glucopyranoseM [auth L]11N/A
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPL
Query on CPL

Download Ideal Coordinates CCD File 
O [auth A],
R [auth C],
S [auth E],
T [auth F]
1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N
PTY
Query on PTY

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P [auth A],
W [auth H]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
ELU (Subject of Investigation/LOI)
Query on ELU

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N [auth A]phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate
C20 H38 O7 P2
SJMIVFIDXGVUHA-WKWVIOPWSA-N
323
Query on 323

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X [auth P]2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate
C25 H22 N2 O4
ZFGLYCCNMJCDCP-UHFFFAOYSA-N
NAG
Query on NAG

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U [auth G],
V [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MN
Query on MN

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Q [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DAB
Query on DAB
I [auth P]L-PEPTIDE LINKINGC4 H10 N2 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 FoundationSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-07
    Type: Initial release
  • Version 2.0: 2023-10-18
    Type: Coordinate replacement
    Reason: Ligand identity
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary