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- PDB-7qig: Infectious mouse-adapted RML scrapie prion fibril purified from t... -

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Basic information

Entry
Database: PDB / ID: 7qig
TitleInfectious mouse-adapted RML scrapie prion fibril purified from terminally-infected mouse brains
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / Prion / Amyloid / PrP / Prion protein / mouse RML scrapie strain / ex vivo prion
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 / positive regulation of glutamate receptor signaling pathway / 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 / lamin binding / positive regulation of glutamate receptor signaling pathway / 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 / negative regulation of dendritic spine maintenance / cupric ion binding / regulation of potassium ion transmembrane transport / 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 / cuprous ion binding / response to amyloid-beta / 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 / 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 / molecular condensate scaffold activity / terminal bouton / protein destabilization / protein homooligomerization / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / regulation of protein localization / amyloid-beta binding / protein-folding chaperone binding / protease binding / microtubule binding / molecular adaptor activity / nuclear membrane / response to oxidative stress / transmembrane transporter binding / learning or memory / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / 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: 2.7 Å
AuthorsManka, S.W. / Zhang, W. / Wenborn, A. / Betts, J. / Joiner, S. / Saibil, H.R. / Collinge, J. / Wadsworth, J.D.F.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U12316055 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00024/5 United Kingdom
Wellcome Trust079605/Z/06/Z United Kingdom
Wellcome Trust101488/Z/13/Z United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: 2.7 Å cryo-EM structure of ex vivo RML prion fibrils.
Authors: Szymon W Manka / Wenjuan Zhang / Adam Wenborn / Jemma Betts / Susan Joiner / Helen R Saibil / John Collinge / Jonathan D F Wadsworth /
Abstract: Mammalian prions propagate as distinct strains and are composed of multichain assemblies of misfolded host-encoded prion protein (PrP). Here, we present a near-atomic resolution cryo-EM structure of ...Mammalian prions propagate as distinct strains and are composed of multichain assemblies of misfolded host-encoded prion protein (PrP). Here, we present a near-atomic resolution cryo-EM structure of PrP fibrils present in highly infectious prion rod preparations isolated from the brains of RML prion-infected mice. We found that prion rods comprise single-protofilament helical amyloid fibrils that coexist with twisted pairs of the same protofilaments. Each rung of the protofilament is formed by a single PrP monomer with the ordered core comprising PrP residues 94-225, which folds to create two asymmetric lobes with the N-linked glycans and the glycosylphosphatidylinositol anchor projecting from the C-terminal lobe. The overall architecture is comparable to that of recently reported PrP fibrils isolated from the brain of hamsters infected with the 263K prion strain. However, there are marked conformational variations that could result from differences in PrP sequence and/or represent distinguishing features of the distinct prion strains.
History
DepositionDec 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 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


Theoretical massNumber of molelcules
Total (without water)45,8703
Polymers45,8703
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 15290.103 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: brain / 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: Amyloid fibril of mouse PrP from RML--infected mouse brain
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse) / Strain: CD-1 / Organ: Brain
Buffer solutionpH: 6.8
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-2/2
VitrificationCryogen name: ETHANE

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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 defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -0.64 ° / Axial rise/subunit: 4.82 Å / Axial symmetry: C1
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119390 / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0053294
ELECTRON MICROSCOPYf_angle_d0.6694461
ELECTRON MICROSCOPYf_dihedral_angle_d6.857444
ELECTRON MICROSCOPYf_chiral_restr0.051456
ELECTRON MICROSCOPYf_plane_restr0.007585

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