7OCI

Cryo-EM structure of yeast Ost6p containing oligosaccharyltransferase complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Functional analysis of Ost3p and Ost6p containing yeast oligosaccharyltransferases.

Neuhaus, J.D.Wild, R.Eyring, J.Irobalieva, R.N.Kowal, J.Lin, C.W.Locher, K.P.Aebi, M.

(2021) Glycobiology 31: 1604-1615

  • DOI: https://doi.org/10.1093/glycob/cwab084
  • Primary Citation of Related Structures:  
    7OCI

  • PubMed Abstract: 

    The oligosaccharyltransferase (OST) is the central enzyme in the N-glycosylation pathway. It transfers a defined oligosaccharide from a lipid-linker onto the asparagine side chain of proteins. The yeast OST consists of eight subunits and exists in two catalytically distinct isoforms that differ in one subunit, Ost3p or Ost6p. The cryo-electron microscopy structure of the Ost6p containing complex was found to be highly similar to the Ost3p containing OST. OST enzymes with altered Ost3p/Ost6p subunits were generated and functionally analyzed. The three C-terminal transmembrane helices were responsible for the higher turnover-rate of the Ost3p vs. the Ost6p containing enzyme in vitro and the more severe hypoglycosylation in Ost3p lacking strains in vivo. Glycosylation of specific OST target sites required the N-terminal thioredoxin domain of Ost3p or Ost6p. This Ost3p/Ost6p dependence was glycosylation site but not protein specific. We concluded that the Ost3p/Ost6p subunits modulate the catalytic activity of OST and provide additional specificity for OST substrate recognition.


Macromolecules
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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))
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UniProt GroupP41543
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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))
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UniProt GroupP46964
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6332Saccharomyces cerevisiae S288CMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q03723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ03723
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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
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UniProt GroupQ99380
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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
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UniProt GroupQ92316
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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
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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
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UniProt GroupP33767
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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
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST6 - TM124Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.4.99.18
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth K]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-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G46836GH
GlyCosmos:  G46836GH
GlyGen:  G46836GH
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP

Download Ideal Coordinates CCD File 
O [auth B],
R [auth D]
Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
V8K
Query on V8K

Download Ideal Coordinates CCD File 
U [auth F]Dolichylphosphate
C55 H91 O4 P
RELQHJGBFDNPMD-MJTCBKSFSA-N
PEE
Query on PEE

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L [auth A]
N [auth B]
P [auth C]
Q [auth D]
T [auth F]
L [auth A],
N [auth B],
P [auth C],
Q [auth D],
T [auth F],
X [auth H]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
NAG
Query on NAG

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M [auth A],
V [auth G],
W [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
S [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.46 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandCRSII5_173709

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release