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Yorodumi- EMDB-2477: Negative stain electron microscopy structure of native human Pres... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2477 | |||||||||
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Title | Negative stain electron microscopy structure of native human Presenilin 1 (PS1) complex | |||||||||
Map data | Native human PS1 complex | |||||||||
Sample |
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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 / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / protein catabolic process at postsynapse / 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 / negative regulation of core promoter binding / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / short-term synaptic potentiation / protein catabolic process at postsynapse / positive regulation of amyloid precursor protein biosynthetic process / positive regulation of endopeptidase activity / Noncanonical activation of NOTCH3 / sequestering of calcium ion / Notch receptor processing / choline transport / central nervous system myelination / synaptic vesicle targeting / membrane protein intracellular domain proteolysis / negative regulation of axonogenesis / regulation of resting membrane potential / T cell activation involved in immune response / NOTCH4 Activation and Transmission of Signal to the Nucleus / skin morphogenesis / growth factor receptor binding / regulation of synaptic vesicle cycle / dorsal/ventral neural tube patterning / neural retina development / L-glutamate import across plasma membrane / myeloid dendritic cell differentiation / Regulated proteolysis of p75NTR / cerebral cortex cell migration / regulation of phosphorylation / metanephros development / brain morphogenesis / endoplasmic reticulum calcium ion homeostasis / nuclear outer membrane / glutamate receptor signaling pathway / locomotion / amyloid precursor protein metabolic process / smooth endoplasmic reticulum calcium ion homeostasis / regulation of canonical Wnt signaling pathway / astrocyte activation involved in immune response / aggresome / regulation of long-term synaptic potentiation / embryonic limb morphogenesis / skeletal system morphogenesis / cell fate specification / ciliary rootlet / myeloid cell homeostasis / regulation of postsynapse organization / azurophil granule membrane / G protein-coupled dopamine receptor signaling pathway / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / positive regulation of amyloid fibril formation / Golgi cisterna membrane / adult behavior / mitochondrial transport / positive regulation of dendritic spine development / positive regulation of receptor recycling / blood vessel development / regulation of neuron projection development / heart looping / protein glycosylation / amyloid precursor protein catabolic process / amyloid-beta formation / negative regulation of apoptotic signaling pathway / membrane protein ectodomain proteolysis / endopeptidase activator activity / autophagosome assembly / EPH-ephrin mediated repulsion of cells / smooth endoplasmic reticulum / neuron development / hematopoietic progenitor cell differentiation / negative regulation of ubiquitin-dependent protein catabolic process / somitogenesis / calcium ion homeostasis / T cell proliferation / Nuclear signaling by ERBB4 / rough endoplasmic reticulum / epithelial cell proliferation / Notch signaling pathway / regulation of synaptic transmission, glutamatergic / neuron projection maintenance / NOTCH2 Activation and Transmission of Signal to the Nucleus / cellular response to calcium ion / astrocyte activation / NOTCH3 Activation and Transmission of Signal to the Nucleus / Degradation of the extracellular matrix / positive regulation of glycolytic process / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / cerebellum development / post-embryonic development / thymus development / negative regulation of protein phosphorylation / dendritic shaft / PDZ domain binding / apoptotic signaling pathway / cell-cell adhesion / synapse organization Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 17.4 Å | |||||||||
Authors | Li Y / Lu S / Tsai CJ / Bohm C / Qamar S / Dodd RB / Meadows W / Jeon A / McLeod A / Chen F ...Li Y / Lu S / Tsai CJ / Bohm C / Qamar S / Dodd RB / Meadows W / Jeon A / McLeod A / Chen F / Arimon M / Berezovska O / Hyman BT / Tomita T / Iwatsubod T / Johnsof CM / Farrer L / Schmitt-Ulms G / Fraser P / St George-Hyslop P | |||||||||
Citation | Journal: Structure / Year: 2014 Title: Structural interactions between inhibitor and substrate docking sites give insight into mechanisms of human PS1 complexes. Authors: Yi Li / Stephen Hsueh-Jeng Lu / Ching-Ju Tsai / Christopher Bohm / Seema Qamar / Roger B Dodd / William Meadows / Amy Jeon / Adam McLeod / Fusheng Chen / Muriel Arimon / Oksana Berezovska / ...Authors: Yi Li / Stephen Hsueh-Jeng Lu / Ching-Ju Tsai / Christopher Bohm / Seema Qamar / Roger B Dodd / William Meadows / Amy Jeon / Adam McLeod / Fusheng Chen / Muriel Arimon / Oksana Berezovska / Bradley T Hyman / Taisuke Tomita / Takeshi Iwatsubo / Christopher M Johnson / Lindsay A Farrer / Gerold Schmitt-Ulms / Paul E Fraser / Peter H St George-Hyslop / Abstract: Presenilin-mediated endoproteolysis of transmembrane proteins plays a key role in physiological signaling and in the pathogenesis of Alzheimer disease and some cancers. Numerous inhibitors have been ...Presenilin-mediated endoproteolysis of transmembrane proteins plays a key role in physiological signaling and in the pathogenesis of Alzheimer disease and some cancers. Numerous inhibitors have been found via library screens, but their structural mechanisms remain unknown. We used several biophysical techniques to investigate the structure of human presenilin complexes and the effects of peptidomimetic γ-secretase inhibitors. The complexes are bilobed. The head contains nicastrin ectodomain. The membrane-embedded base has a central channel and a lateral cleft, which may represent the initial substrate docking site. Inhibitor binding induces widespread structural changes, including rotation of the head and closure of the lateral cleft. These changes block substrate access to the catalytic pocket and inhibit the enzyme. Intriguingly, peptide substrate docking has reciprocal effects on the inhibitor binding site. Similar reciprocal shifts may underlie the mechanisms of other inhibitors and of the "lateral gate" through which substrates access to the catalytic site. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2477.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-2477-v30.xml emd-2477.xml | 11.6 KB 11.6 KB | Display Display | EMDB header |
Images | EMD-2477.png | 65 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2477 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2477 | HTTPS FTP |
-Validation report
Summary document | emd_2477_validation.pdf.gz | 203 KB | Display | EMDB validaton report |
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Full document | emd_2477_full_validation.pdf.gz | 202.1 KB | Display | |
Data in XML | emd_2477_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2477 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2477 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2477.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Native human PS1 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : native human Presenilin 1 (PS1) complex
Entire | Name: native human Presenilin 1 (PS1) complex |
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Components |
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-Supramolecule #1000: native human Presenilin 1 (PS1) complex
Supramolecule | Name: native human Presenilin 1 (PS1) complex / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: 1:1:1:1 / Number unique components: 4 |
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Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Presenilin-1
Macromolecule | Name: Presenilin-1 / type: protein_or_peptide / ID: 1 / Name.synonym: Protein S182 Details: N-terminus as tagged with TAP tag composed of Protein G and Streptavidin binding peptide tags separated by tobacco etch virus protease cleavage site Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: human |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293 |
Sequence | UniProtKB: Presenilin-1 |
-Macromolecule #2: Nicastrin
Macromolecule | Name: Nicastrin / type: protein_or_peptide / ID: 2 / Name.synonym: KIAA0253 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: HEK293 |
Sequence | UniProtKB: Nicastrin |
-Macromolecule #3: Gamma-secretase subunit APH-1A
Macromolecule | Name: Gamma-secretase subunit APH-1A / type: protein_or_peptide / ID: 3 / Name.synonym: Aph-1alpha / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: HEK293 |
Sequence | UniProtKB: Gamma-secretase subunit APH-1A |
-Macromolecule #4: Gamma-secretase subunit PEN-2
Macromolecule | Name: Gamma-secretase subunit PEN-2 / type: protein_or_peptide / ID: 4 / Name.synonym: Presenilin enhancer protein 2 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: HEK293 |
Sequence | UniProtKB: Gamma-secretase subunit PEN-2 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 7.4 Details: 50 mM Tris-HCl, 150 mM NaCl, 2 mM EDTA, 5 mM MgCl2, 5 mM CaCl2 |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on 1% w/v uranyl acetate for 2-10 seconds |
Grid | Details: Carbon-coated 400-mesh copper grids were glow discharged in air at 600-700 V for 30-60 seconds on an Edward S150B sputter coater. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Date | Nov 19, 2009 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Number real images: 300 |
Electron beam | Acceleration voltage: 120 kV / Electron source: TUNGSTEN HAIRPIN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.0 µm |
Sample stage | Specimen holder model: OTHER |
-Image processing
Details | The particles were selected using EMAN2 |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.4 Å / Resolution method: OTHER / Software - Name: EMAN2, RELION / Number images used: 11234 |