6IYC | pdb_00006iyc

Recognition of the Amyloid Precursor Protein by Human gamma-secretase

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6IYC

This is version 3.0 of the entry. See complete history. 

Literature

Recognition of the amyloid precursor protein by human gamma-secretase.

Zhou, R., Yang, G., Guo, X., Zhou, Q., Lei, J., Shi, Y.

(2019) Science 363

  • DOI: https://doi.org/10.1126/science.aaw0930
  • Primary Citation Related Structures: 
    6IYC

  • PubMed Abstract: 

    Cleavage of amyloid precursor protein (APP) by the intramembrane protease γ-secretase is linked to Alzheimer's disease (AD). We report an atomic structure of human γ-secretase in complex with a transmembrane (TM) APP fragment at 2.6-angstrom resolution. The TM helix of APP closely interacts with five surrounding TMs of PS1 (the catalytic subunit of γ-secretase). A hybrid β sheet, which is formed by a β strand from APP and two β strands from PS1, guides γ-secretase to the scissile peptide bond of APP between its TM and β strand. Residues at the interface between PS1 and APP are heavily targeted by recurring mutations from AD patients. This structure, together with that of γ-secretase bound to Notch, reveal contrasting features of substrate binding, which may be applied toward the design of substrate-specific inhibitors.

    • Organizational Affiliation: 
    • Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecule Content 

  • Total Structure Weight: 191.22 kDa 
  • Atom Count: 11,037 
  • Modeled Residue Count: 1,355 
  • Deposited Residue Count: 1,646 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicastrin709Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92542
Glycosylation
Glycosylation Sites: 12
Go to GlyGen: Q92542-1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Presenilin-1467Homo sapiensMutation(s): 1 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49768
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-secretase subunit APH-1A265Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96BI3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-secretase subunit PEN-2101Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZ42
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Amyloid-beta A4 protein104Homo sapiensMutation(s): 1 
Gene Names: APP, A4, AD1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P05067 (Homo sapiens)
Explore P05067 
Go to UniProtKB:  P05067
PHAROS:  P05067
GTEx:  ENSG00000142192 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05067
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, I, J, K
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD 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
G
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G89225LT
GlyCosmos: G89225LT
GlyGen: G89225LT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PC1

Query on PC1


Download:Ideal Coordinates CCD File
R [auth B],
V [auth C]		1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
CLR

Query on CLR


Download:Ideal Coordinates CCD File
S [auth C],
T [auth C],
U [auth C]		CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG

Query on NAG


Download:Ideal Coordinates CCD File
L [auth A]
M [auth A]
N [auth A]
O [auth A]
P [auth A]
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31621092

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.2: 2025-07-02
    Changes: Data collection, Structure summary
  • Version 3.0: 2025-09-17
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary