8X53

Cryo-EM structure of human gamma-secretase in complex with Abeta46


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 mechanism of substrate recognition and cleavage by human gamma-secretase.

Guo, X.Li, H.Yan, C.Lei, J.Zhou, R.Shi, Y.

(2024) Science 384: 1091-1095

  • DOI: https://doi.org/10.1126/science.adn5820
  • Primary Citation of Related Structures:  
    8X52, 8X53, 8X54

  • PubMed Abstract: 

    Successive cleavages of amyloid precursor protein C-terminal fragment with 99 residues (APP-C99) by γ-secretase result in amyloid-β (Aβ) peptides of varying lengths. Most cleavages have a step size of three residues. To elucidate the underlying mechanism, we determined the atomic structures of human γ-secretase bound individually to APP-C99, Aβ49, Aβ46, and Aβ43. In all cases, the substrate displays the same structural features: a transmembrane α-helix, a three-residue linker, and a β-strand that forms a hybrid β-sheet with presenilin 1 (PS1). Proteolytic cleavage occurs just ahead of the substrate β-strand. Each cleavage is followed by unwinding and translocation of the substrate α-helix by one turn and the formation of a new β-strand. This mechanism is consistent with existing biochemical data and may explain the cleavages of other substrates by 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 100084, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicastrin709Homo sapiensMutation(s): 0 
Gene Names: NCSTNKIAA0253UNQ1874/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: 11Go to GlyGen: Q92542-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Presenilin-1467Homo sapiensMutation(s): 0 
Gene Names: PSEN1AD3PS1PSNL1
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
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-secretase subunit APH-1A265Homo sapiensMutation(s): 0 
Gene Names: APH1APSFCGI-78UNQ579/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
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-secretase subunit PEN-2143Homo sapiensMutation(s): 0 
Gene Names: PSENENPEN2MDS033
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 
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UniProt GroupQ9NZ42
Sequence Annotations
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Amyloid-beta precursor protein46Homo sapiensMutation(s): 0 
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  
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UniProt GroupP05067
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D 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 Glycosylation3D 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 (Subject of Investigation/LOI)
Query on PC1

Download Ideal Coordinates CCD File 
R [auth B],
S [auth B],
V [auth C]
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
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: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Basic Research Program of China (973 Program)China2020YFA0509300

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Structure summary