+Open data
-Basic information
Entry | Database: PDB / ID: 4uis | ||||||
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Title | The cryoEM structure of human gamma-Secretase complex | ||||||
Components |
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Keywords | HYDROLASE / GAMMA-SECRETASE | ||||||
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 / 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 / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / adult behavior / positive regulation of receptor recycling / mitochondrial transport / positive regulation of catalytic activity / regulation of neuron projection development / heart looping / 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 / EPH-ephrin mediated repulsion of cells / neuron development / rough endoplasmic reticulum / Nuclear signaling by ERBB4 / 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 / viral release from host cell by cytolysis / 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 / peptidoglycan catabolic 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 / neuron migration Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Sun, L. / Zhao, L. / Yang, G. / Yan, C. / Zhou, R. / Zhou, X. / Xie, T. / Zhao, Y. / Wu, S. / Li, X. / Shi, Y. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2015 Title: Structural basis of human γ-secretase assembly. Authors: Linfeng Sun / Lingyun Zhao / Guanghui Yang / Chuangye Yan / Rui Zhou / Xiaoyuan Zhou / Tian Xie / Yanyu Zhao / Shenjie Wu / Xueming Li / Yigong Shi / Abstract: The four-component intramembrane protease γ-secretase is intricately linked to the development of Alzheimer's disease. Despite recent structural advances, the transmembrane segments (TMs) of γ- ...The four-component intramembrane protease γ-secretase is intricately linked to the development of Alzheimer's disease. Despite recent structural advances, the transmembrane segments (TMs) of γ-secretase remain to be specifically assigned. Here we report a 3D structure of human γ-secretase at 4.32-Å resolution, determined by single-particle, electron cryomicroscopy in the presence of digitonin and with a T4 lysozyme fused to the amino terminus of presenilin 1 (PS1). The overall structure of this human γ-secretase is very similar to that of wild-type γ-secretase determined in the presence of amphipols. The 20 TMs are unambiguously assigned to the four components, revealing principles of subunit assembly. Within the transmembrane region, PS1 is centrally located, with its amino-terminal fragment (NTF) packing against Pen-2 and its carboxyl-terminal fragment (CTF) interacting with Aph-1. The only TM of nicastrin associates with Aph-1 at the thick end of the TM horseshoe, and the extracellular domain of nicastrin directly binds Pen-2 at the thin end. TM6 and TM7 in PS1, which harbor the catalytic aspartate residues, are located on the convex side of the TM horseshoe. This structure serves as an important framework for understanding the function and mechanism of γ-secretase. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4uis.cif.gz | 281.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uis.ent.gz | 235.6 KB | Display | PDB format |
PDBx/mmJSON format | 4uis.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/4uis ftp://data.pdbj.org/pub/pdb/validation_reports/ui/4uis | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 63331.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK 293S / Production host: HOMO SAPIENS (human) / References: UniProt: Q92542*PLUS |
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#2: Protein | Mass: 23547.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK 293S / Production host: HOMO SAPIENS (human) / References: UniProt: P49768*PLUS |
#3: Protein | Mass: 16698.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK 293S / Production host: HOMO SAPIENS (human) |
#4: Protein | Mass: 5294.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK 293S / Production host: HOMO SAPIENS (human) |
#5: Protein | Mass: 18435.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK 293S / Production host: HOMO SAPIENS (human) References: UniProt: A0A097J809, UniProt: D9IEF7*PLUS, lysozyme |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: T4-LYSOZYME FUSION GAMMA- SECRETASE / Type: COMPLEX |
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Buffer solution | Name: 0.1% DIGITONIN, 25 MM HEPES, PH 7.4, AND 150 MM NACL. / pH: 7.4 Details: 0.1% DIGITONIN, 25 MM HEPES, PH 7.4, AND 150 MM NACL. |
Specimen | Conc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 277, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING, |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Dec 22, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 1.4 mm |
Image recording | Electron dose: 4.5 e/Å2 / Film or detector model: DIRECT ELECTRON DE-12 (4k x 3k) |
Image scans | Num. digital images: 2000 |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 4.4 Å / Num. of particles: 177207 / Nominal pixel size: 1.32 Å / Actual pixel size: 1.32 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2974. (DEPOSITION ID: 13293 Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE | ||||||||||||
Atomic model building | PDB-ID: 4R12 | ||||||||||||
Refinement | Highest resolution: 4.4 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.4 Å
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