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- PDB-8efu: a22L prion fibril -

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Basic information

Entry
Database: PDB / ID: 8efu
Titlea22L prion fibril
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / Prion / Fibril / GPI-anchorless / PrP / Infectious / Amyloid / Brain-derived / ex vivo / Prion strain
Function / homology
Function and homology information


Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / nucleobase-containing compound metabolic process / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / response to amyloid-beta / negative regulation of type II interferon production / cuprous ion binding / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / response to cadmium ion / side of membrane / inclusion body / neuron projection maintenance / positive regulation of calcium-mediated signaling / molecular function activator activity / cellular response to copper ion / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein homooligomerization / protein destabilization / cellular response to xenobiotic stimulus / cellular response to amyloid-beta / terminal bouton / positive regulation of neuron apoptotic process / signaling receptor activity / regulation of protein localization / protein-folding chaperone binding / amyloid-beta binding / response to oxidative stress / protease binding / nuclear membrane / microtubule binding / molecular adaptor activity / transmembrane transporter binding / learning or memory / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / metal ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Prion, copper binding octapeptide repeat / Copper binding octapeptide repeat region / Major prion protein N-terminal domain / Major prion protein bPrPp - N terminal / Prion protein signature 1. / Prion protein signature 2. / 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 speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHoyt, F. / Caughey, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI000580-33 United States
CitationJournal: PLoS Pathog / Year: 2022
Title: Cryo-EM of prion strains from the same genotype of host identifies conformational determinants.
Authors: Forrest Hoyt / Parvez Alam / Efrosini Artikis / Cindi L Schwartz / Andrew G Hughson / Brent Race / Chase Baune / Gregory J Raymond / Gerald S Baron / Allison Kraus / Byron Caughey /
Abstract: Prion strains in a given type of mammalian host are distinguished by differences in clinical presentation, neuropathological lesions, survival time, and characteristics of the infecting prion protein ...Prion strains in a given type of mammalian host are distinguished by differences in clinical presentation, neuropathological lesions, survival time, and characteristics of the infecting prion protein (PrP) assemblies. Near-atomic structures of prions from two host species with different PrP sequences have been determined but comparisons of distinct prion strains of the same amino acid sequence are needed to identify purely conformational determinants of prion strain characteristics. Here we report a 3.2 Å resolution cryogenic electron microscopy-based structure of the 22L prion strain purified from the brains of mice engineered to express only PrP lacking glycophosphatidylinositol anchors [anchorless (a) 22L]. Comparison of this near-atomic structure to our recently determined structure of the aRML strain propagated in the same inbred mouse reveals that these two mouse prion strains have distinct conformational templates for growth via incorporation of PrP molecules of the same sequence. Both a22L and aRML are assembled as stacks of PrP molecules forming parallel in-register intermolecular β-sheets and intervening loops, with single monomers spanning the ordered fibril core. Each monomer shares an N-terminal steric zipper, three major arches, and an overall V-shape, but the details of these and other conformational features differ markedly. Thus, variations in shared conformational motifs within a parallel in-register β-stack fibril architecture provide a structural basis for prion strain differentiation within a single host genotype.
History
DepositionSep 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major prion protein
B: Major prion protein
C: Major prion protein
D: Major prion protein
E: Major prion protein


Theoretical massNumber of molelcules
Total (without water)127,7525
Polymers127,7525
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Negative stain transmission electron microscopy, microscopy, Cryo electron tomography
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Major prion protein / PrP / PrP27-30 / PrP33-35C


Mass: 25550.348 Da / Num. of mol.: 5 / Mutation: S233Stop / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P04925
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: GPI anchorless underglycosylated 22L prion fibril / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Organ: Brain
Buffer solutionpH: 7.4
Details: Sample suspended in 20 mM Tris pH 7.4, 100 mM containing 0.02% amphipol 8-35
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 57 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 4449
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10REFMACmodel refinement
11RELION4.0 betainitial Euler assignment
12RELION4.0 betafinal Euler assignment
13RELION4.0 betaclassification
14RELION4.0 beta3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.565 ° / Axial rise/subunit: 4.75 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 226306
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16409
Details: Pixel size was corrected in post processing from 1.1 A/pix to 1.045 A/pix to correct an error in the reported magnification pixel size.
Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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