8PN9

Structure of human oligosaccharyltransferase OST-A complex bound to NGI-1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Positive selection CRISPR screens reveal a druggable pocket in an oligosaccharyltransferase required for inflammatory signaling to NF-kappa B.

Lampson, B.L.Ramirez, A.S.Baro, M.He, L.Hegde, M.Koduri, V.Pfaff, J.L.Hanna, R.E.Kowal, J.Shirole, N.H.He, Y.Doench, J.G.Contessa, J.N.Locher, K.P.Kaelin Jr., W.G.

(2024) Cell 187: 2209-2223.e16

  • DOI: https://doi.org/10.1016/j.cell.2024.03.022
  • Primary Citation of Related Structures:  
    8PN9

  • PubMed Abstract: 

    Nuclear factor κB (NF-κB) plays roles in various diseases. Many inflammatory signals, such as circulating lipopolysaccharides (LPSs), activate NF-κB via specific receptors. Using whole-genome CRISPR-Cas9 screens of LPS-treated cells that express an NF-κB-driven suicide gene, we discovered that the LPS receptor Toll-like receptor 4 (TLR4) is specifically dependent on the oligosaccharyltransferase complex OST-A for N-glycosylation and cell-surface localization. The tool compound NGI-1 inhibits OST complexes in vivo, but the underlying molecular mechanism remained unknown. We did a CRISPR base-editor screen for NGI-1-resistant variants of STT3A, the catalytic subunit of OST-A. These variants, in conjunction with cryoelectron microscopy studies, revealed that NGI-1 binds the catalytic site of STT3A, where it traps a molecule of the donor substrate dolichyl-PP-GlcNAc 2 -Man 9 -Glc 3 , suggesting an uncompetitive inhibition mechanism. Our results provide a rationale for and an initial step toward the development of STT3A-specific inhibitors and illustrate the power of contemporaneous base-editor and structural studies to define drug mechanism of action.


  • Organizational Affiliation

    Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A705Homo sapiensMutation(s): 0 
Gene Names: STT3AITM1TMC
EC: 2.4.99.18
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P46977 (Homo sapiens)
Explore P46977 
Go to UniProtKB:  P46977
PHAROS:  P46977
GTEx:  ENSG00000134910 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46977
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P46977-1
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 437Homo sapiensMutation(s): 0 
Gene Names: OST4
Membrane Entity: Yes 
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Find proteins for P0C6T2 (Homo sapiens)
Explore P0C6T2 
Go to UniProtKB:  P0C6T2
PHAROS:  P0C6T2
GTEx:  ENSG00000228474 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C6T2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Transmembrane protein 25879Homo sapiensMutation(s): 0 
Gene Names: TMEM258C11orf10HSPC005
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P61165 (Homo sapiens)
Explore P61165 
Go to UniProtKB:  P61165
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 
Gene Names: DAD1
Membrane Entity: Yes 
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Find proteins for P61803 (Homo sapiens)
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PHAROS:  P61803
GTEx:  ENSG00000129562 
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UniProt GroupP61803
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 1607Homo sapiensMutation(s): 0 
Gene Names: RPN1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P04843 (Homo sapiens)
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PHAROS:  P04843
GTEx:  ENSG00000163902 
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UniProt GroupP04843
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P04843-1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2631Homo sapiensMutation(s): 0 
Gene Names: RPN2
Membrane Entity: Yes 
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Find proteins for P04844 (Homo sapiens)
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PHAROS:  P04844
GTEx:  ENSG00000118705 
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UniProt GroupP04844
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Oligosaccharyltransferase complex subunit OSTCG [auth H]149Homo sapiensMutation(s): 0 
Gene Names: OSTCDC2HDCMD45PHSPC307
Membrane Entity: Yes 
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Find proteins for Q9NRP0 (Homo sapiens)
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PHAROS:  Q9NRP0
GTEx:  ENSG00000198856 
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UniProt GroupQ9NRP0
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunitH [auth G]452Homo sapiensMutation(s): 1 
Gene Names: DDOSTKIAA0115OST48OK/SW-cl.45
Membrane Entity: Yes 
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Find proteins for P39656 (Homo sapiens)
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Go to UniProtKB:  P39656
PHAROS:  P39656
GTEx:  ENSG00000244038 
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UniProt GroupP39656
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Oligosaccharides

Help

Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
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-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G55220VL
GlyCosmos:  G55220VL
GlyGen:  G55220VL
Entity ID: 12
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-alpha-D-glucopyranose-(1-3)-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-alpha-D-glucopyranoseL [auth N]11N/A
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OTP
Query on OTP

Download Ideal Coordinates CCD File 
Q [auth A](2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE
C40 H68 O7 P2
IKKLDISSULFFQO-DJMILUHSSA-N
EGY
Query on EGY

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O [auth A],
T [auth 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
KZB
Query on KZB

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M [auth A],
N [auth A],
S [auth F],
U [auth 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
ZXT (Subject of Investigation/LOI)
Query on ZXT

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R [auth A]5-(dimethylsulfamoyl)-~{N}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolidin-1-yl-benzamide
C17 H22 N4 O3 S2
QPKGRLIYJGBKJL-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
P [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.61 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 FoundationSwitzerland310030_196862

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary