6S7O

Cryo-EM structure of human oligosaccharyltransferase complex OST-A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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

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
  • Primary Citation of Related Structures:  
    6S7O, 6S7T

  • 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) manner. Here, we present high-resolution cryo-electron microscopy structures of human OST-A and OST-B ...

    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 LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3AA705Homo sapiensMutation(s): 0 
Gene Names: STT3AITM1TMC
EC: 2.4.99.18
Membrane Entity: Yes 
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Find proteins for P46977 (Homo sapiens)
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PHAROS:  P46977
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UniProt GroupP46977
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 4B37Homo sapiensMutation(s): 0 
Gene Names: OST4
Membrane Entity: Yes 
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Find proteins for P0C6T2 (Homo sapiens)
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Go to UniProtKB:  P0C6T2
PHAROS:  P0C6T2
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UniProt GroupP0C6T2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Transmembrane protein 258C79Homo sapiensMutation(s): 0 
Gene Names: TMEM258C11orf10HSPC005
Membrane Entity: Yes 
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PHAROS:  P61165
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UniProt GroupP61165
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1D113Homo sapiensMutation(s): 0 
Gene Names: DAD1
Membrane Entity: Yes 
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UniProt GroupP61803
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1E607Homo sapiensMutation(s): 0 
Gene Names: RPN1
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2F631Homo sapiensMutation(s): 0 
Gene Names: RPN2
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunitG456Homo sapiensMutation(s): 0 
Gene Names: DDOSTKIAA0115OST48OK/SW-cl.45
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Oligosaccharyltransferase complex subunit OSTCH149Homo sapiensMutation(s): 0 
Gene Names: OSTCDC2HDCMD45PHSPC307
Membrane Entity: Yes 
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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/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 10
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseJ 8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G81980VO
GlyCosmos:  G81980VO
GlyGen:  G81980VO
Entity ID: 11
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
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-glucopyranoseK 8N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EGY
Query on EGY

Download Ideal Coordinates CCD File 
CA [auth F],
O [auth A],
P [auth A],
S [auth C],
T [auth C],
CA [auth F],
O [auth A],
P [auth A],
S [auth C],
T [auth C],
U [auth D],
X [auth E]
(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

Download Ideal Coordinates CCD File 
AA [auth F],
BA [auth F],
DA [auth G],
L [auth A],
M [auth A],
AA [auth F],
BA [auth F],
DA [auth G],
L [auth A],
M [auth A],
N [auth A],
V [auth E],
W [auth E],
Z [auth F]
(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
KZE
Query on KZE

Download Ideal Coordinates CCD File 
R [auth A][(3~{R},6~{Z},10~{Z},14~{Z},18~{Z})-3,7,11,15,19,23-hexamethyltetracosa-6,10,14,18,22-pentaenyl] dihydrogen phosphate
C30 H53 O4 P
QHBZVPDZRJSJAI-IFQOQNDLSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
Q [auth A],
Y [auth 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  (Full details and data files)

  • 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