+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24514 | |||||||||
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Title | Cryo-EM structure of human PrP23-144 amyloid fibrils | |||||||||
Map data | PrP23-144 amyloid fibrils | |||||||||
Sample |
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Keywords | Prion / amyloid / PROTEIN FIBRIL | |||||||||
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 / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production ...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 / glycosaminoglycan binding / ATP-dependent protein binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / NCAM1 interactions / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of protein processing / negative regulation of calcineurin-NFAT signaling cascade / dendritic spine maintenance / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / extrinsic component of membrane / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / 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 / tubulin binding / negative regulation of protein phosphorylation / molecular condensate scaffold activity / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / postsynapse / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / transmembrane transporter binding / molecular adaptor activity / postsynaptic density / learning or memory / regulation of cell cycle / membrane raft / cell cycle / 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 / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.86 Å | |||||||||
Authors | Li Q / Surewicz WK | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Cryo-EM structure of disease-related prion fibrils provides insights into seeding barriers. Authors: Qiuye Li / Christopher P Jaroniec / Witold K Surewicz / Abstract: One of the least understood aspects of prion diseases is the structure of infectious prion protein aggregates. Here we report a high-resolution cryo-EM structure of amyloid fibrils formed by human ...One of the least understood aspects of prion diseases is the structure of infectious prion protein aggregates. Here we report a high-resolution cryo-EM structure of amyloid fibrils formed by human prion protein with the Y145Stop mutation that is associated with a familial prion disease. This structural insight allows us not only to explain previous biochemical findings, but also provides direct support for the conformational adaptability model of prion transmissibility barriers. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24514.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-24514-v30.xml emd-24514.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | emd_24514.png | 149.3 KB | ||
Filedesc metadata | emd-24514.cif.gz | 4.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24514 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24514 | HTTPS FTP |
-Validation report
Summary document | emd_24514_validation.pdf.gz | 365.6 KB | Display | EMDB validaton report |
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Full document | emd_24514_full_validation.pdf.gz | 365.2 KB | Display | |
Data in XML | emd_24514_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_24514_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24514 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24514 | HTTPS FTP |
-Related structure data
Related structure data | 7rl4MC 8djaC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24514.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | PrP23-144 amyloid fibrils | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : PrP23-144 amyloid fibrils
Entire | Name: PrP23-144 amyloid fibrils |
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Components |
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-Supramolecule #1: PrP23-144 amyloid fibrils
Supramolecule | Name: PrP23-144 amyloid fibrils / 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: 20 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.541743 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSDPKKRPKP GGWNTGGSRY PGQGSPGGNR YPPQGGGGWG QPHGGGWGQP HGGGWGQPHG GGWGQPHGGG WGQGGGTHSQ WNKPSKPKT NMKHMAGAAA AGAVVGGLGG YMLGSAMSRP IIHFGSD 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: 6.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.71 Å Applied symmetry - Helical parameters - Δ&Phi: -2.41 ° Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic) Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46803 |
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Startup model | Type of model: NONE |
Final angle assignment | Type: NOT APPLICABLE |