7Y5X | pdb_00007y5x

CryoEM structure of PS2-containing gamma-secretase treated with MRK-560

PDB DOI: https://doi.org/10.2210/pdb7Y5X/pdb
EM Map EMD-33628: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2022-06-17 Released: 2022-11-02
Deposition Author(s): Guo, X., Wang, Y., Zhou, J., Jin, C., Wang, J., Jia, B., Jing, D., Yan, C., Lei, J., Zhou, R., Shi, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Molecular basis for isoform-selective inhibition of presenilin-1 by MRK-560.

Guo, X., Wang, Y., Zhou, J., Jin, C., Wang, J., Jia, B., Jing, D., Yan, C., Lei, J., Zhou, R., Shi, Y.

(2022) Nat Commun 13: 6299-6299

PubMed: 36272978 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-33817-5
Primary Citation Related Structures:
7Y5T, 7Y5X, 7Y5Z

PubMed Abstract:
Inhibition of γ-secretase activity represents a potential therapeutic strategy for Alzheimer's disease (AD). MRK-560 is a selective inhibitor with higher potency for Presenilin 1 (PS1) than for PS2, the two isoforms of the catalytic subunit of γ-secretase, although the underlying mechanism remains elusive. Here we report the cryo-electron microscopy (cryo-EM) structures of PS1 and PS2-containing γ-secretase complexes with and without MRK-560 at overall resolutions of 2.9-3.4 Å. MRK-560 occupies the substrate binding site of PS1, but is invisible in PS2. Structural comparison identifies Thr281 and Leu282 in PS1 to be the determinant for isoform-dependent sensitivity to MRK-560, which is confirmed by swapping experiment between PS1 and PS2. By revealing the mechanism for isoform-selective inhibition of presenilin, our work may facilitate future drug discovery targeting γ-secretase.

Organizational Affiliation

Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Key Laboratory for Protein Sciences of Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China.

Macromolecule Content

Total Structure Weight: 176.81 kDa
Atom Count: 10,016
Modeled Residue Count: 1,216
Deposited Residue Count: 1,523
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nicastrin	A	709	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92542
Glycosylation
Glycosylation Sites: 11	Glycosylation Focus chain A	Go to GlyGen: Q92542-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Presenilin-2	B	448	Homo sapiens	Mutation(s): 0 Gene Names: PSEN2, AD4, PS2, PSNL2, STM2 EC: 3.4.23 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P49810 (Homo sapiens) Explore P49810 Go to UniProtKB: P49810
PHAROS: P49810 GTEx: ENSG00000143801
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49810
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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, UNQ1874/PRO4317 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96BI3
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NZ42
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	D 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC1 Query on PC1 Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth A]	Q [auth A], R [auth B]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth B] Interactions & Density Focus chain Q [auth A] Focus chain R [auth B]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [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 P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]