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Yorodumi- PDB-7qig: Infectious mouse-adapted RML scrapie prion fibril purified from t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qig | |||||||||||||||
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Title | Infectious mouse-adapted RML scrapie prion fibril purified from terminally-infected mouse brains | |||||||||||||||
Components | Major prion protein | |||||||||||||||
Keywords | PROTEIN 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 / lamin binding / 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 / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / lamin binding / 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 / regulation of potassium ion transmembrane transport / negative regulation of interleukin-17 production / negative regulation of dendritic spine maintenance / type 5 metabotropic glutamate receptor binding / cupric ion binding / nucleobase-containing compound metabolic process / response to copper ion / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / activation of protein kinase activity / cuprous ion binding / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / response to amyloid-beta / : / negative regulation of type II interferon production / intracellular copper ion homeostasis / negative regulation of long-term synaptic potentiation / positive regulation of protein targeting to membrane / side of membrane / response to cadmium ion / regulation of peptidyl-tyrosine phosphorylation / inclusion body / cellular response to copper ion / neuron projection maintenance / protein sequestering activity / tubulin binding / negative regulation of protein phosphorylation / molecular condensate scaffold activity / molecular function activator activity / positive regulation of protein localization to plasma membrane / protein destabilization / protein homooligomerization / negative regulation of DNA-binding transcription factor activity / terminal bouton / cellular response to amyloid-beta / regulation of protein localization / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / signaling receptor activity / amyloid-beta binding / protein-folding chaperone binding / microtubule binding / nuclear membrane / protease binding / response to oxidative stress / mitochondrial outer membrane / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / learning or memory / membrane raft / copper ion binding / intracellular membrane-bounded organelle / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) | |||||||||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||
Authors | Manka, S.W. / Zhang, W. / Wenborn, A. / Betts, J. / Joiner, S. / Saibil, H.R. / Collinge, J. / Wadsworth, J.D.F. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qig.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qig.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 7qig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/7qig ftp://data.pdbj.org/pub/pdb/validation_reports/qi/7qig | HTTPS FTP |
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-Related structure data
Related structure data | 13989MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-10992 (Title: Infectious mouse-adapted RML scrapie prion fibrils purified from terminally-infected mouse brains Data size: 1.0 TB Data #1: Aligned multi-frame micrographs of RML prion fibrils [micrographs - single frame]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Amyloid fibril of mouse PrP from RML--infected mouse brain Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mus musculus (house mouse) / Strain: CD-1 / Organ: Brain |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -0.64 ° / Axial rise/subunit: 4.82 Å / Axial symmetry: C1 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119390 / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
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