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- EMDB-7017: Segment from bank vole prion protein 168-176 QYNNQNNFV -

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Basic information

Entry
Database: EMDB / ID: EMD-7017
TitleSegment from bank vole prion protein 168-176 QYNNQNNFV
Map dataprotein segment
Sample
  • Complex: bank vole prion 168-176
    • Protein or peptide: Major prion protein
  • Ligand: water
Keywordspolar clasp / amyloid fibril / prion / PROTEIN FIBRIL
Function / homology
Function and homology information


side of membrane / protein homooligomerization / Golgi apparatus / plasma membrane
Similarity search - Function
Prion protein signature 1. / Prion protein signature 2. / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein / Major prion protein / Prion/Doppel protein, beta-ribbon domain / Prion/Doppel beta-ribbon domain superfamily / Prion/Doppel alpha-helical domain
Similarity search - Domain/homology
Biological speciesMyodes glareolus (Bank vole)
Methodelectron crystallography / cryo EM
AuthorsGlynn C / Rodriguez JA
CitationJournal: Nat Struct Mol Biol / Year: 2018
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
DepositionSep 7, 2017-
Header (metadata) releaseNov 1, 2017-
Map releaseJan 17, 2018-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.44
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.44
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6axz
  • Surface level: 0.44
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7017.png

Downloads & links

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Map

FileDownload / File: emd_7017.map.gz / Format: CCP4 / Size: 484.4 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprotein segment
Voxel sizeX: 0.22455 Å / Y: 0.235 Å / Z: 0.24336 Å
Density
Contour LevelBy AUTHOR: 0.44 / Movie #1: 0.44
Minimum - Maximum-0.719746 - 3.6190872
Average (Standard dev.)-0.000000000425498 (±0.3238952)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions2212844
Spacing2244128
CellA: 4.94 Å / B: 10.34 Å / C: 31.15 Å
α: 94.205 ° / β: 92.375 ° / γ: 102.204 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.224545454545450.2350.243359375
M x/y/z2244128
origin x/y/z0.0000.0000.000
length x/y/z4.94010.34031.150
α/β/γ94.20592.375102.204
start NX/NY/NZ000
NX/NY/NZ2244128
MAP C/R/S312
start NC/NR/NS000
NC/NR/NS1282244
D min/max/mean-0.7203.619-0.000

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Supplemental data

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Sample components

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Entire : bank vole prion 168-176

EntireName: bank vole prion 168-176
Components
  • Complex: bank vole prion 168-176
    • Protein or peptide: Major prion protein
  • Ligand: water

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Supramolecule #1: bank vole prion 168-176

SupramoleculeName: bank vole prion 168-176 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Myodes glareolus (Bank vole)
Molecular weightTheoretical: 4.6 KDa

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Macromolecule #1: Major prion protein

MacromoleculeName: Major prion protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Myodes glareolus (Bank vole)
Molecular weightTheoretical: 1.140162 KDa
SequenceString:
QYNNQNNFV

UniProtKB: Major prion protein

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Camera length: 950 mm
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 0.025 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Crystallography statisticsNumber 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
Final reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: AB INITIO MODEL / Overall B value: 6.068 / Target criteria: maximum likelihood
Output model

PDB-6axz:
Segment from bank vole prion protein 168-176 QYNNQNNFV

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