8KCU

Cryo-EM structure of human gamma-secretase in complex with MK-0752

PDB DOI: https://doi.org/10.2210/pdb8KCU/pdb
EM Map EMD-37110: 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
Deposition Author(s): Guo, X., Li, H., Kai, U., Yan, C., Lei, J., Zhou, R., Shi, Y.
Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural 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.

Macromolecule Content

Total Structure Weight: 178.94 kDa
Atom Count: 10,833
Modelled Residue Count: 1,313
Deposited Residue Count: 1,534
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Presenilin-1	A [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 Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicastrin	B [auth A]	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	Glycosylation Focus chain B [auth A]	Go to GlyGen: Q92542-1
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-secretase subunit APH-1A	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 Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-secretase subunit PEN-2	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 Annotations Expand
Reference Sequence

Oligosaccharides

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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	Interactions Focus chain E Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain E Focus chain G Focus chain H Focus chain I Focus chain J
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	Interactions Focus chain F Interactions & Density Focus chain F
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 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain V [auth C] MOL2 format, chain K [auth B] MOL2 format, chain V [auth C]	K [auth B], V [auth C]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain K [auth B] Focus chain V [auth C] Interactions & Density Focus chain K [auth B] Focus chain V [auth C]
OL9 (Subject of Investigation/LOI) Query on OL9 Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	L [auth B]	3-[4-[2,5-bis(fluoranyl)phenyl]-4-(4-chlorophenyl)sulfonyl-cyclohexyl]propanoic acid C₂₁ H₂₁ Cl F₂ O₄ S XCGJIFAKUZNNOR-QCKZDCLWSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C]	S [auth C], T [auth C], U [auth C]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A]	M [auth A] N [auth A] O [auth A] P [auth A] Q [auth A] M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]