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: https://doi.org/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. 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A705Homo sapiensMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
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Find proteins for P46977 (Homo sapiens)
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PHAROS:  P46977
GTEx:  ENSG00000134910 
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UniProt GroupP46977
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 437Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P0C6T2 (Homo sapiens)
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Go to UniProtKB:  P0C6T2
PHAROS:  P0C6T2
GTEx:  ENSG00000228474 
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UniProt GroupP0C6T2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein 25879Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  P61165
GTEx:  ENSG00000134825 
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UniProt GroupP61165
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1113Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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PHAROS:  P61803
GTEx:  ENSG00000129562 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1607Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000163902 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2631Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000118705 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit456Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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GTEx:  ENSG00000244038 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Oligosaccharyltransferase complex subunit OSTC149Homo sapiensMutation(s): 0 
Gene Names: OSTC, DC2, HDCMD45P, HSPC307
Membrane Entity: Yes 
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GTEx:  ENSG00000198856 
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Oligosaccharides

Help

Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
3N/A
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
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)-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
J
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81980VO
GlyCosmos:  G81980VO
GlyGen:  G81980VO
Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D 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-glucopyranose
K
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Small Molecules
Ligands 4 Unique
IDChains Name / 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
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
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
MG
Query on MG
Download Ideal Coordinates CCD File 
Q [auth A],
Y [auth E]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

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