+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20900 | |||||||||
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Title | human prion protein fibril, M129 variant | |||||||||
Map data | Human prion protein fibril, M129 variant | |||||||||
Sample |
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Keywords | amyloid / fibril / prion / filament / protein fibril / fiber / PrP | |||||||||
Function / homology | Function and homology information positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions ...positive regulation of glutamate receptor signaling pathway / negative regulation of amyloid precursor protein catabolic process / lamin binding / regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / negative regulation of dendritic spine maintenance / glycosaminoglycan binding / ATP-dependent protein binding / NCAM1 interactions / negative regulation of interleukin-17 production / regulation of potassium ion transmembrane transport / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of membrane / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of interleukin-2 production / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / cuprous ion binding / response to amyloid-beta / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / long-term memory / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / tubulin binding / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to amyloid-beta / cellular response to xenobiotic stimulus / protein-folding chaperone binding / signaling receptor activity / amyloid-beta binding / microtubule binding / protease binding / nuclear membrane / transmembrane transporter binding / response to oxidative stress / postsynapse / molecular adaptor activity / postsynaptic density / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / external side of plasma membrane / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Glynn C / Sawaya MR | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core. Authors: Calina Glynn / Michael R Sawaya / Peng Ge / Marcus Gallagher-Jones / Connor W Short / Ronquiajah Bowman / Marcin Apostol / Z Hong Zhou / David S Eisenberg / Jose A Rodriguez / Abstract: Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease- ...Self-templating assemblies of the human prion protein are clinically associated with transmissible spongiform encephalopathies. Here we present the cryo-EM structure of a denaturant- and protease-resistant fibril formed in vitro spontaneously by a 9.7-kDa unglycosylated fragment of the human prion protein. This human prion fibril contains two protofilaments intertwined with screw symmetry and linked by a tightly packed hydrophobic interface. Each protofilament consists of an extended beta arch formed by residues 106 to 145 of the prion protein, a hydrophobic and highly fibrillogenic disease-associated segment. Such structures of prion polymorphs serve as blueprints on which to evaluate the potential impact of sequence variants on prion disease. | |||||||||
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_20900.map.gz | 171.9 MB | EMDB map data format | |
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Header (meta data) | emd-20900-v30.xml emd-20900.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_20900.png | 79.2 KB | ||
Filedesc metadata | emd-20900.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20900 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20900 | HTTPS FTP |
-Validation report
Summary document | emd_20900_validation.pdf.gz | 362.6 KB | Display | EMDB validaton report |
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Full document | emd_20900_full_validation.pdf.gz | 362.2 KB | Display | |
Data in XML | emd_20900_validation.xml.gz | 7.5 KB | Display | |
Data in CIF | emd_20900_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20900 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20900 | HTTPS FTP |
-Related structure data
Related structure data | 6uurMC 6pq5C 6pqaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_20900.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human prion protein fibril, M129 variant | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 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 : Fiber of human prion protein
Entire | Name: Fiber of human prion protein |
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Components |
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-Supramolecule #1: Fiber of human prion protein
Supramolecule | Name: Fiber of human prion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Major prion protein
Macromolecule | Name: Major prion protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 9.685771 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GTHSQWNKPS KPKTNMKHMA GAAAAGAVVG GLGGYMLGSA MSRPIIHFGS DYEDRYYREN MHRYPNQVYY RPMDEYSNQN NFVHD UniProtKB: Major prion protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 2.4 Å Applied symmetry - Helical parameters - Δ&Phi: 179.3 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 76246 |
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Startup model | Type of model: NONE / Details: Gaussian cylinder |
Final angle assignment | Type: NOT APPLICABLE |