[English] 日本語
Yorodumi- EMDB-3061: Cryo-EM structure of the human gamma-secretase complex at 3.4 ang... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3061 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the human gamma-secretase complex at 3.4 angstrom resolution. | |||||||||
Map data | 3D cryo-EM reconstruction of the human gamma-secretase complex at 3.4 angstrom resolution. | |||||||||
Sample |
| |||||||||
Keywords | cryo-EM / human gamma-secretase / membrane protein / single particle | |||||||||
Function / homology | Function and homology information 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 / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / positive regulation of amyloid precursor protein biosynthetic process ...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 / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / positive regulation of amyloid precursor protein biosynthetic process / Noncanonical activation of NOTCH3 / positive regulation of endopeptidase activity / choline transport / Notch receptor processing / central nervous system myelination / sequestering of calcium ion / membrane protein intracellular domain proteolysis / synaptic vesicle targeting / negative regulation of axonogenesis / regulation of resting membrane potential / T cell activation involved in immune response / skin morphogenesis / NOTCH4 Activation and Transmission of Signal to the Nucleus / growth factor receptor binding / neural retina development / dorsal/ventral neural tube patterning / regulation of synaptic vesicle cycle / L-glutamate import across plasma membrane / myeloid dendritic cell differentiation / Regulated proteolysis of p75NTR / amyloid precursor protein metabolic process / regulation of phosphorylation / metanephros development / locomotion / brain morphogenesis / glutamate receptor signaling pathway / endoplasmic reticulum calcium ion homeostasis / nuclear outer membrane / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / regulation of canonical Wnt signaling pathway / aggresome / regulation of long-term synaptic potentiation / embryonic limb morphogenesis / skeletal system morphogenesis / positive regulation of amyloid fibril formation / cell fate specification / regulation of postsynapse organization / positive regulation of dendritic spine development / ciliary rootlet / myeloid cell homeostasis / azurophil granule membrane / dopamine receptor signaling pathway / adult behavior / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / Golgi cisterna membrane / positive regulation of receptor recycling / mitochondrial transport / positive regulation of catalytic activity / heart looping / regulation of neuron projection development / blood vessel development / amyloid precursor protein catabolic process / cerebral cortex cell migration / smooth endoplasmic reticulum / protein glycosylation / amyloid-beta formation / negative regulation of apoptotic signaling pathway / autophagosome assembly / membrane protein ectodomain proteolysis / endopeptidase activator activity / EPH-ephrin mediated repulsion of cells / neuron development / Nuclear signaling by ERBB4 / rough endoplasmic reticulum / hematopoietic progenitor cell differentiation / somitogenesis / amyloid-beta metabolic process / T cell proliferation / negative regulation of ubiquitin-dependent protein catabolic process / Notch signaling pathway / regulation of synaptic transmission, glutamatergic / NOTCH2 Activation and Transmission of Signal to the Nucleus / cellular response to calcium ion / neuron projection maintenance / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Degradation of the extracellular matrix / cerebellum development / positive regulation of glycolytic process / post-embryonic development / dendritic shaft / thymus development / negative regulation of protein phosphorylation / epithelial cell proliferation / PDZ domain binding / NOTCH3 Activation and Transmission of Signal to the Nucleus / astrocyte activation / apoptotic signaling pathway / synapse organization Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.4 Å | |||||||||
Authors | Bai XC / Yan CY / Yang GH / Lu PL / Ma D / Sun LF / Zhou R / Scheres SHW / Shi YG | |||||||||
Citation | Journal: Nature / Year: 2015 Title: An atomic structure of human γ-secretase. Authors: Xiao-Chen Bai / Chuangye Yan / Guanghui Yang / Peilong Lu / Dan Ma / Linfeng Sun / Rui Zhou / Sjors H W Scheres / Yigong Shi / Abstract: Dysfunction of the intramembrane protease γ-secretase is thought to cause Alzheimer's disease, with most mutations derived from Alzheimer's disease mapping to the catalytic subunit presenilin 1 (PS1) ...Dysfunction of the intramembrane protease γ-secretase is thought to cause Alzheimer's disease, with most mutations derived from Alzheimer's disease mapping to the catalytic subunit presenilin 1 (PS1). Here we report an atomic structure of human γ-secretase at 3.4 Å resolution, determined by single-particle cryo-electron microscopy. Mutations derived from Alzheimer's disease affect residues at two hotspots in PS1, each located at the centre of a distinct four transmembrane segment (TM) bundle. TM2 and, to a lesser extent, TM6 exhibit considerable flexibility, yielding a plastic active site and adaptable surrounding elements. The active site of PS1 is accessible from the convex side of the TM horseshoe, suggesting considerable conformational changes in nicastrin extracellular domain after substrate recruitment. Component protein APH-1 serves as a scaffold, anchoring the lone transmembrane helix from nicastrin and supporting the flexible conformation of PS1. Ordered phospholipids stabilize the complex inside the membrane. Our structure serves as a molecular basis for mechanistic understanding of γ-secretase function. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3061.map.gz | 20.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-3061-v30.xml emd-3061.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | EMD-3061.jpg | 222.6 KB | ||
Others | EMD-3061-full.map EMD-3061-half-1.map EMD-3061-half-2.map | 22.2 MB 22.2 MB 22.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3061 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3061 | HTTPS FTP |
-Related structure data
Related structure data | 5a63MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10194 (Title: An atomic structure of human gamma-secretase / Data size: 11.7 TB Data #1: Unaligned multi-frame micrographs of human gamma-secretase [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_3061.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 3D cryo-EM reconstruction of the human gamma-secretase complex at 3.4 angstrom resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Supplemental map: EMD-3061-full.map
File | EMD-3061-full.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Supplemental map: EMD-3061-half-1.map
File | EMD-3061-half-1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Supplemental map: EMD-3061-half-2.map
File | EMD-3061-half-2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : human gamma-secretase
Entire | Name: human gamma-secretaseGamma secretase |
---|---|
Components |
|
-Supramolecule #1000: human gamma-secretase
Supramolecule | Name: human gamma-secretase / type: sample / ID: 1000 / Oligomeric state: heterotetramer / Number unique components: 4 |
---|---|
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 |
---|---|
Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: HEK 293F cells / Location in cell: membrane |
Molecular weight | Experimental: 170 KDa / Theoretical: 170 KDa |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK 293F cells / Recombinant plasmid: pMLink |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL |
---|---|
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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 81000 |
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 |
Date | Oct 2, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 2925 / Average electron dose: 38 e/Å2 Details: 20 frames were recorded by the direct electron detector |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION / Number images used: 159549 |
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. |