|Entry||Database: EMDB / ID: 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||human gamma-secretaseGamma secretase:|
|Keywords||cryo-EM / human gamma-secretase / membrane protein / single particle|
|Function / homology||Gamma-secretase subunit Aph-1 / Nicastrin / Degradation of the extracellular matrix / Regulated proteolysis of p75NTR / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Presenilin/signal peptide peptidase / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus ...Gamma-secretase subunit Aph-1 / Nicastrin / Degradation of the extracellular matrix / Regulated proteolysis of p75NTR / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Presenilin/signal peptide peptidase / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / EPH-ephrin mediated repulsion of cells / Peptidase A22A, presenilin 1 / Peptidase A22A, presenilin / Nicastrin / Presenilin / Aph-1 protein / Neutrophil degranulation / NOTCH3 Activation and Transmission of Signal to the Nucleus / NOTCH4 Activation and Transmission of Signal to the Nucleus / Noncanonical activation of NOTCH3 / Amyloid fiber formation / Nuclear signaling by ERBB4 / positive regulation of L-glutamate import across plasma membrane / Cajal-Retzius cell differentiation / positive regulation of coagulation / amyloid precursor protein biosynthetic process / amyloid precursor protein catabolic process / positive regulation of amyloid precursor protein biosynthetic process / aspartic endopeptidase activity, intramembrane cleaving / Notch receptor processing, ligand-dependent / short-term synaptic potentiation / regulation of resting membrane potential / gamma-secretase complex / negative regulation of core promoter binding / choline transport / synaptic vesicle targeting / Notch receptor processing / T cell activation involved in immune response / neural retina development / central nervous system myelination / epithelial cell proliferation / amyloid-beta formation / dorsal/ventral neural tube patterning / regulation of long-term synaptic potentiation / membrane protein intracellular domain proteolysis / glutamate receptor signaling pathway / brain morphogenesis / amyloid precursor protein metabolic process / skin morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / metanephros development / regulation of phosphorylation / endoplasmic reticulum calcium ion homeostasis / dopamine receptor signaling pathway / myeloid dendritic cell differentiation / nuclear outer membrane / positive regulation of receptor recycling / regulation of canonical Wnt signaling pathway / regulation of neuron projection development / negative regulation of axonogenesis / adult behavior / somitogenesis / azurophil granule membrane / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / positive regulation of amyloid fibril formation / cell fate specification / negative regulation of ubiquitin-protein transferase activity / embryonic limb morphogenesis / skeletal system morphogenesis / positive regulation of dendritic spine development / ciliary rootlet / myeloid cell homeostasis / autophagosome assembly / hematopoietic progenitor cell differentiation / aggresome / cerebral cortex cell migration / heart looping / blood vessel development / negative regulation of ubiquitin-dependent protein catabolic process / Hydrolases, Acting on peptide bonds (peptidases), Aspartic endopeptidases / T cell proliferation / negative regulation of apoptotic signaling pathway / modulation of age-related behavioral decline / Golgi cisterna membrane / smooth endoplasmic reticulum / mitochondrial transport / activation of MAPKK activity / protein glycosylation / neuron development / positive regulation of catalytic activity / cerebellum development / calcium channel activity / membrane protein ectodomain proteolysis / synapse organization / regulation of synaptic transmission, glutamatergic / post-embryonic development / protein processing / kinetochore / regulation of synaptic plasticity|
Function and homology information
|Source||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / 3.4 Å resolution|
|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
|Validation Report||PDB-ID: 5a63|
SummaryFull reportAbout validation report
|Date||Deposition: Jun 23, 2015 / Header (metadata) release: Jul 1, 2015 / Map release: Aug 12, 2015 / Last update: Sep 9, 2015|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3061.map.gz (map file in CCP4 format, 22783 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.4 Å|
CCP4 map header:
-Entire human gamma-secretase
|Entire||Name: human gamma-secretase / Number of components: 4 / Oligomeric State: heterotetramer|
|Mass||Theoretical: 170 kDa / Experimental: 170 kDa|
-Component #1: protein, gamma-secretase
|Protein||Name: gamma-secretaseGamma secretase / Oligomeric Details: Heterotetramer / Recombinant expression: Yes / Number of Copies: 1|
|Mass||Theoretical: 170 kDa / Experimental: 170 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Homo sapiens (human) / Vector: pMLink / Cell of expression system: HEK 293F cells|
|Source (natural)||Location in cell: membrane / Cell: HEK 293F cells|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 6 mg/ml|
Buffer solution: 25 mM HEPES, pH 7.4, 150 mM NaCl and amphipol A8-35
|Support film||300 mesh Au 1.2/1.3 Quantifoil grid, glow discharged for 1 minute|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 85 K / Humidity: 100 % / Method: Blot for 4 seconds before plunging|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: Oct 2, 2014|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 38 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 81000 X (nominal), 35714 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3200 nm / Energy filter: Gatan Quantum / Energy window: 0-20 eV|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 85 K ( 80 - 90 K)|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 2925 / Sampling size: 5 microns|
Details: 20 frames were recorded by the direct electron detector
|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])
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 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.
|3D reconstruction||Software: CTFFIND3, RELION / CTF correction: Each particle / Resolution: 3.4 Å / Resolution method: FSC 0.143, gold-standard|
-Atomic model buiding
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