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- PDB-7yat: CryoEM tetra protofilament structure of the hamster prion 108-144... -

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Basic information

Entry
Database: PDB / ID: 7yat
TitleCryoEM tetra protofilament structure of the hamster prion 108-144 fibril
ComponentsMajor prion protein
KeywordsPROTEIN FIBRIL / Prion / fibril / hamster
Function / homology
Function and homology information


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 / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / negative regulation of calcineurin-NFAT signaling cascade ...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 / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / 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 / negative regulation of type II interferon production / cuprous ion binding / positive regulation of protein targeting to membrane / 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 / presynapse / signaling receptor activity / amyloid-beta binding / response to oxidative stress / protease binding / nuclear membrane / microtubule binding / amyloid fibril formation / learning or memory / regulation of cell cycle / 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 / identical protein binding / 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 speciesMesocricetus auratus (golden hamster)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsChen, E.H.-L. / Kao, S.-W. / Lee, C.-H. / Huang, J.Y.C. / Chen, R.P.-Y. / Wu, K.-P.
Funding support Taiwan, 5items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-CDA-110-L03 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 105-2119-M-001-028 Taiwan
Ministry of Science and Technology (MoST, Taiwan)106-2923-M-001-003-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)109-2113-M-001-001 Taiwan
Ministry of Science and Technology (MoST, Taiwan)MOST 109-2311-B-001-022 Taiwan
CitationJournal: J Am Chem Soc / Year: 2022
Title: 2.2 Å Cryo-EM Tetra-Protofilament Structure of the Hamster Prion 108-144 Fibril Reveals an Ordered Water Channel in the Center.
Authors: Eric H-L Chen / Hsi-Wen Kao / Chih-Hsuan Lee / Jessica Y C Huang / Kuen-Phon Wu / Rita P-Y Chen /
Abstract: Fibrils of the hamster prion peptide (sHaPrP, sequence 108-144) were prepared in an acidic solution, and their structure was solved by cryogenic electron microscopy with a resolution of 2.23 Å based ...Fibrils of the hamster prion peptide (sHaPrP, sequence 108-144) were prepared in an acidic solution, and their structure was solved by cryogenic electron microscopy with a resolution of 2.23 Å based on the gold-standard Fourier shell correlation (FSC) curve. The fibril has a novel architecture that has never been found in other amyloid fibrils. Each fibril is assembled by four protofilaments (PFs) and has an ordered water channel in the center. Each protofilament contains three β-strands (125-130, 133-135, and 138-141) arranged in an "R"-shaped construct. The structural data indicate that these three β-strand segments are the most amyloidogenic region of the prion peptide/protein and might be the site of nucleation during fibrillization under conditions without denaturants.
History
DepositionJun 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 17, 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 1.3Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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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
C: Major prion protein
D: Major prion protein
E: Major prion protein
F: Major prion protein
G: Major prion protein
H: Major prion protein
I: Major prion protein
J: Major prion protein
K: Major prion protein
L: Major prion protein
M: Major prion protein
N: Major prion protein
O: Major prion protein
P: Major prion protein
Q: Major prion protein
R: Major prion protein
S: Major prion protein
T: Major prion protein
U: Major prion protein
V: Major prion protein
X: Major prion protein
Y: Major prion protein


Theoretical massNumber of molelcules
Total (without water)59,99924
Polymers59,99924
Non-polymers00
Water45025
1


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

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Components

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


Mass: 2499.955 Da / Num. of mol.: 24 / Source method: obtained synthetically / Source: (synth.) Mesocricetus auratus (golden hamster) / References: UniProt: P04273
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster prion 108-144 fibril reveals an ordered water channel in the center
Type: TISSUE / Entity ID: #1 / Source: SYNTHETIC
Molecular weightExperimental value: NO
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Buffer solutionpH: 3.7
SpecimenEmbedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
4CTFFIND4CTF correction
7PHENIXmodel fitting
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: -1.76 ° / Axial rise/subunit: 4.77 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 2368403
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 336759 / Symmetry type: HELICAL
Atomic model buildingB value: 21.9 / Protocol: AB INITIO MODEL / Space: REAL

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