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- EMDB-3239: Cryo-EM structure of gamma secretase in class 2 of the apo-state ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-3239 | |||||||||
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Title | Cryo-EM structure of gamma secretase in class 2 of the apo-state ensemble | |||||||||
![]() | Reconstruction of gamma secretase in class 2 of the apo-state ensemble | |||||||||
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Function / homology | ![]() Cajal-Retzius cell differentiation / positive regulation of L-glutamate import across plasma membrane / amyloid precursor protein biosynthetic process / positive regulation of coagulation / protein catabolic process at postsynapse / negative regulation of core promoter binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bai XC / Rajendra E / Yang GH / Shi YG / Scheres SHW | |||||||||
![]() | ![]() Title: Sampling the conformational space of the catalytic subunit of human γ-secretase. Authors: Xiao-chen Bai / Eeson Rajendra / Guanghui Yang / Yigong Shi / Sjors H W Scheres / ![]() ![]() Abstract: Human γ-secretase is an intra-membrane protease that cleaves many different substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein ...Human γ-secretase is an intra-membrane protease that cleaves many different substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein lead to Alzheimer's disease. Our previous cryo-EM structure of γ-secretase revealed considerable disorder in its catalytic subunit presenilin. Here, we describe an image classification procedure that characterizes molecular plasticity at the secondary structure level, and apply this method to identify three distinct conformations in our previous sample. In one of these conformations, an additional transmembrane helix is visible that cannot be attributed to the known components of γ-secretase. In addition, we present a γ-secretase structure in complex with the dipeptidic inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT). Our results reveal how conformational mobility in the second and sixth transmembrane helices of presenilin is greatly reduced upon binding of DAPT or the additional helix, and form the basis for a new model of how substrate enters the transmembrane domain. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.1 KB 10.1 KB | Display Display | ![]() |
Images | ![]() | 223.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fn4MC ![]() 3237C ![]() 3238C ![]() 3240C ![]() 5fn2C ![]() 5fn3C ![]() 5fn5C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Reconstruction of gamma secretase in class 2 of the apo-state ensemble | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : human gamma secretase in class 2 of the apo-state ensemble
Entire | Name: human gamma secretase in class 2 of the apo-state ensemble![]() |
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Components |
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-Supramolecule #1000: human gamma secretase in class 2 of the apo-state ensemble
Supramolecule | Name: human gamma secretase in class 2 of the apo-state ensemble type: sample / ID: 1000 / Oligomeric state: Heterotetramer / Number unique components: 1 |
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Molecular weight | Experimental: 170 KDa / Theoretical: 170 KDa |
-Macromolecule #1: gamma-secretase
Macromolecule | Name: gamma-secretase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Heterotetramer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 170 KDa / Theoretical: 170 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | ![]() ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 7.4 Details: 25 mM HEPES, pH 7.4, 150 mM NaCl and amphipol A8-35 |
Staining | Type: NEGATIVE / Details: cryo-EM |
Grid | Details: 300 mesh Au 1.2/1.3 Quantifoil grid, glow discharged for 1 minute |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 85 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 4 seconds before plunging |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Energy filter - Name: Gatan Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Temperature | Min: 80 K / Max: 90 K / Average: 85 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 81000 magnification |
Date | Oct 25, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 2925 / Average electron dose: 38 e/Å2 Details: Use a newly developed statistical movie processing and particle polishing approach to compensate for beam-induced movement and reduce the effect of radiation-damage |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Software - Name: CTFFIND4, RELION / Number images used: 79263 |