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- EMDB-33719: CryoEM tetra protofilament structure of the hamster prion 108-144... -
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Open data
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Basic information
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Title | CryoEM tetra protofilament structure of the hamster prion 108-144 fibril | ||||||||||||||||||
![]() | Cryo-EM map of hamster prion 108-144 fibril, sharpened map. | ||||||||||||||||||
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![]() | Prion / fibril / hamster / PROTEIN FIBRIL | ||||||||||||||||||
Function / homology | ![]() regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of calcineurin-NFAT signaling cascade ...regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / : / negative regulation of type II interferon production / positive regulation of protein targeting to membrane / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / 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 / 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 / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / amyloid fibril formation / learning or memory / regulation of cell cycle / membrane raft / cell cycle / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.2 Å | ||||||||||||||||||
![]() | Chen EH-L / Kao S-W / Lee C-H / Huang JYC / Chen RP-Y / Wu K-P | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: 2.2 Å Cryo-EM Tetra-Protofilament Structure of the Hamster Prion 108-144 Fibril Reveals an Ordered Water Channel in the Center. Authors: Eric H-L Chen / Hsi-Wen Kao / Chih-Hsuan Lee / Jessica Y C Huang / Kuen-Phon Wu / Rita P-Y Chen / ![]() Abstract: Fibrils of the hamster prion peptide (sHaPrP, sequence 108-144) were prepared in an acidic solution, and their structure was solved by cryogenic electron microscopy with a resolution of 2.23 Å based ...Fibrils of the hamster prion peptide (sHaPrP, sequence 108-144) were prepared in an acidic solution, and their structure was solved by cryogenic electron microscopy with a resolution of 2.23 Å based on the gold-standard Fourier shell correlation (FSC) curve. The fibril has a novel architecture that has never been found in other amyloid fibrils. Each fibril is assembled by four protofilaments (PFs) and has an ordered water channel in the center. Each protofilament contains three β-strands (125-130, 133-135, and 138-141) arranged in an "R"-shaped construct. The structural data indicate that these three β-strand segments are the most amyloidogenic region of the prion peptide/protein and might be the site of nucleation during fibrillization under conditions without denaturants. | ||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 7.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.9 KB 15.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 104.4 KB | ||
Filedesc metadata | ![]() | 4.8 KB | ||
Others | ![]() ![]() | 65.6 MB 65.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 623.1 KB | Display | ![]() |
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Full document | ![]() | 622.7 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 22.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yatMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Cryo-EM map of hamster prion 108-144 fibril, sharpened map. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM map of hamster prion 108-144 fibril, half map.
File | emd_33719_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM map of hamster prion 108-144 fibril, half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM map of hamster prion 108-144 fibril, half map.
File | emd_33719_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM map of hamster prion 108-144 fibril, half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster...
Entire | Name: 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster prion 108-144 fibril reveals an ordered water channel in the center |
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Components |
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-Supramolecule #1: 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster...
Supramolecule | Name: 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster prion 108-144 fibril reveals an ordered water channel in the center type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Major prion protein
Macromolecule | Name: Major prion protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 2.499955 KDa |
Sequence | String: GAVVGGLGGY MLGSAMSRPM MHFGN UniProtKB: Major prion protein |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 25 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 3.7 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 21.9 |
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Output model | ![]() PDB-7yat: |