6S7T

Cryo-EM structure of human oligosaccharyltransferase complex OST-B


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report



Literature

Cryo-electron microscopy structures of human oligosaccharyltransferase complexes OST-A and OST-B.

Ramirez, A.S.Kowal, J.Locher, K.P.

(2019) Science 366: 1372-1375

  • DOI: 10.1126/science.aaz3505
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan onto secretory proteins in the endoplasmic reticulum. Mammals express two distinct OST complexes that act in a cotranslational (OST-A) or posttranslocational (OST-B) mann ...

    Oligosaccharyltransferase (OST) catalyzes the transfer of a high-mannose glycan onto secretory proteins in the endoplasmic reticulum. Mammals express two distinct OST complexes that act in a cotranslational (OST-A) or posttranslocational (OST-B) manner. Here, we present high-resolution cryo-electron microscopy structures of human OST-A and OST-B. Although they have similar overall architectures, structural differences in the catalytic subunits STT3A and STT3B facilitate contacts to distinct OST subunits, DC2 in OST-A and MAGT1 in OST-B. In OST-A, interactions with TMEM258 and STT3A allow ribophorin-I to form a four-helix bundle that can bind to a translating ribosome, whereas the equivalent region is disordered in OST-B. We observed an acceptor peptide and dolichylphosphate bound to STT3B, but only dolichylphosphate in STT3A, suggesting distinct affinities of the two OST complexes for protein substrates.


    Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH), CH-8093 Zürich, Switzerland. locher@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3BA826Homo sapiensMutation(s): 0 
Gene Names: STT3BSIMP
EC: 2.4.99.18
Find proteins for Q8TCJ2 (Homo sapiens)
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PHAROS  Q8TCJ2
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  • Reference Sequence
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PEPTIDEK7Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4B37Homo sapiensMutation(s): 0 
Gene Names: OST4
Find proteins for P0C6T2 (Homo sapiens)
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PHAROS  P0C6T2
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Transmembrane protein 258C79Homo sapiensMutation(s): 0 
Gene Names: TMEM258C11orf10HSPC005
Find proteins for P61165 (Homo sapiens)
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PHAROS  P61165
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1D113Homo sapiensMutation(s): 0 
Gene Names: DAD1
Find proteins for P61803 (Homo sapiens)
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PHAROS  P61803
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1E607Homo sapiensMutation(s): 0 
Gene Names: RPN1
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PHAROS  P04843
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2F631Homo sapiensMutation(s): 0 
Gene Names: RPN2
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PHAROS  P04844
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunitG456Homo sapiensMutation(s): 0 
Gene Names: DDOSTKIAA0115OST48OK/SW-cl.45
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PHAROS  P39656
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Magnesium transporter protein 1H335Homo sapiensMutation(s): 0 
Gene Names: MAGT1IAG2PSEC0084UNQ628/PRO1244
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PHAROS  Q9H0U3
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
MalectinI292Homo sapiensMutation(s): 0 
Gene Names: MLECKIAA0152
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  • Reference Sequence
Oligosaccharides
Entity ID: 11
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, M
2 N-Glycosylation
Entity ID: 12
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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
L
8 N-Glycosylation
Entity ID: 13
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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
N
8 N-Glycosylation
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0K3
Query on 0K3

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A
(2Z,6Z,10Z,14Z,18Z,22Z,26Z)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl dihydrogen phosphate
C40 H67 O4 P
KVTNIWHEHVWGJC-DLTKSLTJSA-N
 Ligand Interaction
EGY
Query on EGY

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A, C, D, E, F
(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
KZB
Query on KZB

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A, C, D, E, F, G
(2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R},3~{R},4~{R},5'~{S},6~{S},7~{R},8~{S},9~{R},12~{R},13~{R},15~{S},16~{S},18~{R})-5',7,9,13-tetramethyl-3,15-bis(oxidanyl)spiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosane-6,2'-oxane]-16-yl]oxy-oxane-3,4,5-triol
C33 H54 O10
PDUIOILJOMOEIH-KWMFFDLQSA-N
 Ligand Interaction
MG
Query on MG

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A, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 FoundationSwitzerlandCRSII3_147632

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary