9K95 | pdb_00009k95

Cryo-EM structure of human gamma-secretase in complex with compound E

PDB DOI: https://doi.org/10.2210/pdb9K95/pdb
EM Map EMD-62188: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-10-25 Released: 2025-10-29
Deposition Author(s): Zhou, R., Huang, G., Guo, X., Wang, J., Ge, X., Shi, Y.
Funding Organization(s): National Basic Research Program of China (973 Program)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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 insights into human signal peptide peptidase

Zhou, R., Huang, G., Guo, X., Wang, J., Ge, X., Shi, Y.

To be published.

Macromolecule Content

Total Structure Weight: 179.84 kDa
Atom Count: 10,823
Modeled Residue Count: 1,311
Deposited Residue Count: 1,542
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 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
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 A	Go to GlyGen: Q92542-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Presenilin-1	B	467	Homo sapiens	Mutation(s): 0 Gene Names: PSEN1, AD3, PS1, PSNL1 EC: 3.4.23
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: 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
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
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 Q [auth B] SDF format, chain V [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C]	Q [auth B], V [auth C]	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₈ N O₈ P NRJAVPSFFCBXDT-HUESYALOSA-N		Interactions Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain Q [auth B] Focus chain V [auth C]
A1D6X (Subject of Investigation/LOI) Query on A1D6X Download Ideal Coordinates CCD File SDF format, chain R [auth B] MOL2 format, chain R [auth B] mmCIF format, chain R [auth B]	R [auth B]	(2~{S})-2-[2-[3,5-bis(fluoranyl)phenyl]ethanoylamino]-~{N}-[(3~{S})-1-methyl-2-oxidanylidene-5-phenyl-3~{H}-1,4-benzodiazepin-3-yl]propanamide C₂₇ H₂₄ F₂ N₄ O₃ JNGZXGGOCLZBFB-IVCQMTBJSA-N		Interactions Focus chain R [auth B] Interactions & Density Focus chain R [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] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF 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 K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [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] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [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]