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- PDB-8dja: Cryo-EM structure of mouse PrP23-144 amyloid fibrils (polymorph 1) -

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Basic information

Entry
Database: PDB / ID: 8dja
TitleCryo-EM structure of mouse PrP23-144 amyloid fibrils (polymorph 1)
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / moPrP23-144 / amyloid / prion diseases
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 / positive regulation of glutamate receptor signaling pathway / lamin binding / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / type 5 metabotropic glutamate receptor 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 / positive regulation of glutamate receptor signaling pathway / lamin binding / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / ATP-dependent protein binding / type 5 metabotropic glutamate receptor binding / negative regulation of interleukin-17 production / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / cupric ion binding / nucleobase-containing compound metabolic process / activation of protein kinase activity / 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 / cuprous ion binding / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / intracellular copper ion homeostasis / regulation of peptidyl-tyrosine phosphorylation / negative regulation of protein phosphorylation / response to cadmium ion / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / positive regulation of calcium-mediated signaling / molecular function activator activity / positive regulation of protein localization to plasma membrane / negative regulation of DNA-binding transcription factor activity / molecular condensate scaffold activity / terminal bouton / protein destabilization / protein homooligomerization / positive regulation of neuron apoptotic process / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / cellular response to xenobiotic stimulus / signaling receptor activity / regulation of protein localization / amyloid-beta binding / protein-folding chaperone binding / protease binding / microtubule binding / nuclear membrane / molecular adaptor activity / transmembrane transporter binding / response to oxidative stress / learning or memory / postsynaptic density / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
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: 3.92 Å
AuthorsLi, Q. / Surewicz, W.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094357 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS103848 United States
CitationJournal: 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
DepositionJun 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 8, 2023Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major prion protein
B: Major prion protein
K: Major prion protein
P: Major prion protein
C: Major prion protein
G: Major prion protein
L: Major prion protein
Q: Major prion protein
D: Major prion protein
H: Major prion protein
M: Major prion protein
R: Major prion protein
E: Major prion protein
I: Major prion protein
N: Major prion protein
S: Major prion protein
F: Major prion protein
J: Major prion protein
O: Major prion protein
T: Major prion protein


Theoretical massNumber of molelcules
Total (without water)247,97220
Polymers247,97220
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 12398.579 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prnp, Prn-p, Prp / Production host: Escherichia coli (E. coli) / References: UniProt: P04925

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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: Amyloid fibrils formed by moPrP23-144 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -2.36 ° / Axial rise/subunit: 4.74 Å / Axial symmetry: C2
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10628 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0064680
ELECTRON MICROSCOPYf_angle_d1.0176260
ELECTRON MICROSCOPYf_dihedral_angle_d7.559700
ELECTRON MICROSCOPYf_chiral_restr0.05680
ELECTRON MICROSCOPYf_plane_restr0.018800

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