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- EMDB-39574: Cryo-EM structure of human gamma-secretase in complex with Abeta43 -

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Basic information

Entry
Database: EMDB / ID: EMD-39574
TitleCryo-EM structure of human gamma-secretase in complex with Abeta43
Map data
Sample
  • Complex: Cryo-EM structure of human gamma-secretase in complex with Abeta43
    • Other: Abeta43
KeywordsIntramembrane protease / gamma-secretase / MEMBRANE PROTEIN / MEMBRANE PROTEIN-HYDROLASE complex
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsGuo X / Zhou R / Shi Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)National Basic Research Program of China (973 Program) China
CitationJournal: Science / Year: 2024
Title: Molecular mechanism of substrate recognition and cleavage by human γ-secretase.
Authors: Xuefei Guo / Haotian Li / Chuangye Yan / Jianlin Lei / Rui Zhou / Yigong Shi /
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 ...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.
History
DepositionMar 26, 2024-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39574.png

Downloads & links

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Map

FileDownload / File: emd_39574.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0979 Å
Density
Contour LevelBy AUTHOR: 0.36
Minimum - Maximum-0.9469157 - 2.308714
Average (Standard dev.)0.014473358 (±0.071095146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 210.79681 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39574_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39574_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of human gamma-secretase in complex with Abeta43

EntireName: Cryo-EM structure of human gamma-secretase in complex with Abeta43
Components
  • Complex: Cryo-EM structure of human gamma-secretase in complex with Abeta43
    • Other: Abeta43

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Supramolecule #1: Cryo-EM structure of human gamma-secretase in complex with Abeta43

SupramoleculeName: Cryo-EM structure of human gamma-secretase in complex with Abeta43
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Abeta43

MacromoleculeName: Abeta43 / type: other / ID: 1 / Classification: other
Source (natural)Organism: synthetic construct (others)
SequenceString:
DAEFRHDSGY EVHHQKLVFF AEDVGSNKGA IIGLMVGGVV IAT

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

0957

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 578094
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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