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- EMDB-17779: Structure of human oligosaccharyltransferase OST-A complex bound ... -
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Open data
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Basic information
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Title | Structure of human oligosaccharyltransferase OST-A complex bound to NGI-1 | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
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Method | ![]() ![]() | |||||||||
![]() | Ramirez AS / Kowal J / Locher KP | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Positive selection CRISPR screens reveal a druggable pocket in an oligosaccharyltransferase required for inflammatory signaling to NF-κB. Authors: Benjamin L Lampson / Ana S Ramίrez / Marta Baro / Lixia He / Mudra Hegde / Vidyasagar Koduri / Jamie L Pfaff / Ruth E Hanna / Julia Kowal / Nitin H Shirole / Yanfeng He / John G Doench / ...Authors: Benjamin L Lampson / Ana S Ramίrez / Marta Baro / Lixia He / Mudra Hegde / Vidyasagar Koduri / Jamie L Pfaff / Ruth E Hanna / Julia Kowal / Nitin H Shirole / Yanfeng He / John G Doench / Joseph N Contessa / Kaspar P Locher / William G Kaelin / ![]() ![]() 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 ...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-Man-Glc, 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. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 483.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.8 KB 25.8 KB | Display Display | ![]() |
Images | ![]() | 86.8 KB | ||
Filedesc metadata | ![]() | 8.6 KB | ||
Others | ![]() ![]() | 475.7 MB 475.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pn9MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.648 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17779_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17779_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : OLIGOSACCHARYLTRANSFERASE COMPLEX OST-A WITH BOUND NGI-1 INHIBITOR
+Supramolecule #1: OLIGOSACCHARYLTRANSFERASE COMPLEX OST-A WITH BOUND NGI-1 INHIBITOR
+Macromolecule #1: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #2: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #3: Transmembrane protein 258
+Macromolecule #4: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #5: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #6: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase su...
+Macromolecule #7: Oligosaccharyltransferase complex subunit OSTC
+Macromolecule #8: Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48...
+Macromolecule #13: (2~{S},3~{R},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-6-[(1~{S},2~{R}...
+Macromolecule #14: (4R,7R)-4-hydroxy-N,N,N-trimethyl-4,9-dioxo-7-[(undecanoyloxy)met...
+Macromolecule #15: MANGANESE (II) ION
+Macromolecule #16: (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRI...
+Macromolecule #17: 5-(dimethylsulfamoyl)-~{N}-(5-methyl-1,3-thiazol-2-yl)-2-pyrrolid...
+Macromolecule #18: water
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.2 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101699 |