Download MendeleyStructural Basis of gamma-secretase inhibition by anti-cancer clinical drugs
Guo, X., Li, H., Kai, U., Yan, C., Lei, J., Zhou, R., Shi, Y.To be published.
8KCT
Cryo-EM structure of human gamma-secretase in complex with Nirogacestat
- PDB DOI: https://doi.org/10.2210/pdb8KCT/pdb
- EM Map EMD-37109: EMDB EMDataResource
- Classification: MEMBRANE PROTEIN
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No
- Membrane Protein: Yes PDBTM
- Deposited: 2023-08-08 Released: 2024-08-14
- Funding Organization(s): National Basic Research Program of China (973 Program)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.60 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
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Nicastrin | 701 | Homo sapiens | Mutation(s): 0 Gene Names: NCSTN, KIAA0253, UNQ1874/PRO4317 Membrane Entity: Yes |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q92542 (Homo sapiens) Explore Q92542 Go to UniProtKB: Q92542 | |||||
PHAROS: Q92542 GTEx: ENSG00000162736 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q92542 | ||||
Glycosylation | |||||
| Glycosylation Sites: 12 | Go to GlyGen: Q92542-1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Gamma-secretase subunit APH-1A | B [auth C] | 265 | Homo sapiens | Mutation(s): 0 Gene Names: APH1A, PSF, CGI-78, UNQ579/PRO1141 Membrane Entity: Yes |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q96BI3 (Homo sapiens) Explore Q96BI3 Go to UniProtKB: Q96BI3 | |||||
PHAROS: Q96BI3 GTEx: ENSG00000117362 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q96BI3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Gamma-secretase subunit PEN-2 | C [auth D] | 101 | Homo sapiens | Mutation(s): 0 Gene Names: PSENEN, PEN2, MDS033 Membrane Entity: Yes |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9NZ42 (Homo sapiens) Explore Q9NZ42 Go to UniProtKB: Q9NZ42 | |||||
PHAROS: Q9NZ42 GTEx: ENSG00000205155 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9NZ42 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Presenilin-1 | D [auth B] | 467 | Homo sapiens | Mutation(s): 0 Gene Names: PSEN1, AD3, PS1, PSNL1 EC: 3.4.23 Membrane Entity: Yes |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P49768 (Homo sapiens) Explore P49768 Go to UniProtKB: P49768 | |||||
PHAROS: P49768 GTEx: ENSG00000080815 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P49768 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 5 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, G, H, I, J | 2 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT | |||||
Entity ID: 6 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-mannopyranose-(1-3)-[beta-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 | F | 5 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G89225LT GlyCosmos: G89225LT GlyGen: G89225LT | |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PC1 Query on PC1 | T [auth C], U [auth B] | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N |  | ||
| O6U (Subject of Investigation/LOI) Query on O6U | V [auth B] | Nirogacestat C27 H41 F2 N5 O VFCRKLWBYMDAED-REWPJTCUSA-N |  | ||
| CLR Query on CLR | Q [auth C], R [auth C], S [auth C] | CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N |  | ||
| NAG Query on NAG | K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.60 Å
- Aggregation State: PARTICLE
- Reconstruction Method: SINGLE PARTICLE
Entry History & Funding Information
Deposition Data
- Released Date: 2024-08-14 Deposition Author(s): Guo, X., Li, H., Kai, U., Yan, C., Lei, J., Zhou, R., Shi, Y.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Basic Research Program of China (973 Program) | China | 2020YFA0509300 |
Revision History (Full details and data files)
- Version 1.0: 2024-08-14
Type: Initial release - Version 1.1: 2024-11-20
Changes: Advisory, Data collection, Derived calculations, Structure summary
