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


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 STT3B826Homo sapiensMutation(s): 0 
EC: 2.4.99.18
Membrane Entity: Yes 
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PHAROS:  Q8TCJ2
GTEx:  ENSG00000163527 
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UniProt GroupQ8TCJ2
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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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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
Magnesium transporter protein 1335Homo sapiensMutation(s): 0 
Gene Names: MAGT1, IAG2, PSEC0084, UNQ628/PRO1244
Membrane Entity: Yes 
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GTEx:  ENSG00000102158 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Malectin292Homo sapiensMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q14165 (Homo sapiens)
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GTEx:  ENSG00000110917 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PEPTIDEJ [auth K]7Homo sapiensMutation(s): 0 
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Oligosaccharides

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Entity ID: 11
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J],
M		2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 12
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
L
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81980VO
GlyCosmos:  G81980VO
GlyGen:  G81980VO
Entity ID: 13
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
N
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ
GlyCosmos:  G80966KZ
GlyGen:  G80966KZ
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0K3
Query on 0K3
Download Ideal Coordinates CCD File 
W [auth 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
EGY
Query on EGY
Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
IA [auth F]
O [auth A]
P [auth A]
AA [auth D],
EA [auth E],
IA [auth F],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
X [auth C]
(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 
BA [auth D]
CA [auth D]
DA [auth D]
FA [auth E]
GA [auth E]
BA [auth D],
CA [auth D],
DA [auth D],
FA [auth E],
GA [auth E],
JA [auth F],
KA [auth F],
LA [auth F],
MA [auth G],
NA [auth G],
U [auth A],
Y [auth C],
Z [auth C]
(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
MG
Query on MG
Download Ideal Coordinates CCD File 
HA [auth E],
V [auth A]		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

View Full Validation Report



View more in-depth experimental data
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