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 2.0 of the entry. See complete history. 


Literature

Structure of the yeast oligosaccharyltransferase complex gives insight into eukaryotic N-glycosylation.

Wild, R., Kowal, J., Eyring, J., Ngwa, E.M., Aebi, M., Locher, K.P.

(2018) Science 359: 545-550

  • DOI: 10.1126/science.aar5140
  • Primary Citation of Related Structures:  
    6EZN

  • PubMed Abstract: 

    • Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to glycosylation sites of secretory proteins. Here we describe the atomic structure of yeast OST determined by cryo-electron microscopy, revealing a conserved subunit arrangement ...

    Oligosaccharyltransferase (OST) is an essential membrane protein complex in the endoplasmic reticulum, where it transfers an oligosaccharide from a dolichol-pyrophosphate-activated donor to glycosylation sites of secretory proteins. Here we describe the atomic structure of yeast OST determined by cryo-electron microscopy, revealing a conserved subunit arrangement. The active site of the catalytic STT3 subunit points away from the center of the complex, allowing unhindered access to substrates. The dolichol-pyrophosphate moiety binds to a lipid-exposed groove of STT3, whereas two noncatalytic subunits and an ordered N-glycan form a membrane-proximal pocket for the oligosaccharide. The acceptor polypeptide site faces an oxidoreductase domain in stand-alone OST complexes or is immediately adjacent to the translocon, suggesting how eukaryotic OSTs efficiently glycosylate a large number of polypeptides before their folding.

    Organizational Affiliation: 

    Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland. markus.aebi@micro.biol.ethz.ch locher@mol.biol.ethz.ch.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1A476Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST1, NLT1, YJL002C, J1404
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST2B130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST2, YOR103C, YOR3211C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 3C350Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST3, YOR085W, YOR3124W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4D36Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST4, YDL232W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST5E86Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: OST5, YGL226C-A, YGL226BC
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3F718Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STT3, YGL022W
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit WBP1G430Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: WBP1, YEL002C
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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit SWP1H286Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SWP1, YMR149W, YM9375.19
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
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 9
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ, L 2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 11
MoleculeChainsChain Length2D DiagramGlycosylation3D 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-glucopyranoseK 8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G83582BK
GlyCosmos:  G83582BK
GlyGen:  G83582BK
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPL
Query on CPL
Download Ideal Coordinates CCD File 
M [auth A],
N [auth E],
O [auth F],
R [auth H]		1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C42 H80 N O8 P
JLPULHDHAOZNQI-ZTIMHPMXSA-N		 Ligand Interaction
PTY
Query on PTY
Download Ideal Coordinates CCD File 
P [auth F]PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
Q [auth G]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: 3.30 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

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