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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7017 | |||||||||
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Title | Segment from bank vole prion protein 168-176 QYNNQNNFV | |||||||||
![]() | protein segment | |||||||||
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![]() | polar clasp / amyloid fibril / prion / PROTEIN FIBRIL | |||||||||
Function / homology | ![]() side of membrane / protein homooligomerization / Golgi apparatus / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | electron crystallography / cryo EM | |||||||||
![]() | Glynn C / Rodriguez JA | |||||||||
![]() | ![]() Title: Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp. Authors: Marcus Gallagher-Jones / Calina Glynn / David R Boyer / Michael W Martynowycz / Evelyn Hernandez / Jennifer Miao / Chih-Te Zee / Irina V Novikova / Lukasz Goldschmidt / Heather T McFarlane / ...Authors: Marcus Gallagher-Jones / Calina Glynn / David R Boyer / Michael W Martynowycz / Evelyn Hernandez / Jennifer Miao / Chih-Te Zee / Irina V Novikova / Lukasz Goldschmidt / Heather T McFarlane / Gustavo F Helguera / James E Evans / Michael R Sawaya / Duilio Cascio / David S Eisenberg / Tamir Gonen / Jose A Rodriguez / ![]() ![]() Abstract: The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution ...The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 448.6 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.5 KB 10.5 KB | Display Display | ![]() |
Images | ![]() | 185.4 KB | ||
Filedesc metadata | ![]() | 4.3 KB | ||
Filedesc structureFactors | ![]() | 123 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6axzMC ![]() 7287C ![]() 6btkC 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 | protein segment | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X: 0.22455 Å / Y: 0.235 Å / Z: 0.24336 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : bank vole prion 168-176
Entire | Name: bank vole prion 168-176 |
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Components |
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-Supramolecule #1: bank vole prion 168-176
Supramolecule | Name: bank vole prion 168-176 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 4.6 KDa |
-Macromolecule #1: Major prion protein
Macromolecule | Name: Major prion protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.140162 KDa |
Sequence | String: QYNNQNNFV UniProtKB: Major prion protein |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 2 / 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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![]() | electron crystallography |
Aggregation state | 3D array |
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Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.025 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 950 mm |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution method: DIFFRACTION PATTERN/LAYERLINES |
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Crystallography statistics | Number intensities measured: 43252 / Number structure factors: 7474 / Fourier space coverage: 97.1 / R sym: 23.2 / R merge: 23.2 / Overall phase error: 0.01 / Overall phase residual: 0.01 / Phase error rejection criteria: 0 / High resolution: 0.75 Å / Shell - Shell ID: 1 / Shell - High resolution: 0.75 Å / Shell - Low resolution: 0.77 Å / Shell - Number structure factors: 532 / Shell - Phase residual: 0.01 / Shell - Fourier space coverage: 96.2 / Shell - Multiplicity: 4.4 |
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 6.068 / Target criteria: maximum likelihood |
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Output model | ![]() PDB-6axz: |