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- EMDB-33719: CryoEM tetra protofilament structure of the hamster prion 108-144... -

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Basic information

Entry
Database: EMDB / ID: EMD-33719
TitleCryoEM tetra protofilament structure of the hamster prion 108-144 fibril
Map dataCryo-EM map of hamster prion 108-144 fibril, sharpened map.
Sample
  • Tissue: 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster prion 108-144 fibril reveals an ordered water channel in the center
    • Protein or peptide: Major prion protein
  • Ligand: water
KeywordsPrion / fibril / hamster / PROTEIN FIBRIL
Function / homology
Function and homology information


regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / negative regulation of dendritic spine maintenance / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of calcineurin-NFAT signaling cascade ...regulation of glutamate receptor signaling pathway / regulation of calcium ion import across plasma membrane / aspartic-type endopeptidase inhibitor activity / glycosaminoglycan binding / negative regulation of interleukin-17 production / type 5 metabotropic glutamate receptor binding / negative regulation of dendritic spine maintenance / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production / negative regulation of amyloid-beta formation / negative regulation of activated T cell proliferation / cuprous ion binding / negative regulation of type II interferon production / positive regulation of protein targeting to membrane / side of membrane / inclusion body / cellular response to copper ion / neuron projection maintenance / negative regulation of protein phosphorylation / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / terminal bouton / cellular response to amyloid-beta / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of neuron apoptotic process / cellular response to xenobiotic stimulus / presynapse / signaling receptor activity / amyloid-beta binding / microtubule binding / protease binding / nuclear membrane / response to oxidative stress / amyloid fibril formation / learning or memory / regulation of cell cycle / membrane raft / copper ion binding / dendrite / protein-containing complex binding / negative regulation of apoptotic process / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein 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 speciesMesocricetus auratus (golden hamster)
Methodhelical reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsChen EH-L / Kao S-W / Lee C-H / Huang JYC / Chen RP-Y / Wu K-P
Funding support Taiwan, 5 items
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, 2022-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33719.png

Downloads & links

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Map

FileDownload / File: emd_33719.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of hamster prion 108-144 fibril, sharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å		0.83 Å/pix.
x 280 pix.
= 232.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0137
Minimum - Maximum-0.07479385 - 0.12725517
Average (Standard dev.)0.0000094048455 (±0.0024759083)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 232.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM map of hamster prion 108-144 fibril, half map.

Fileemd_33719_half_map_1.map
AnnotationCryo-EM map of hamster prion 108-144 fibril, half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM map of hamster prion 108-144 fibril, half map.

Fileemd_33719_half_map_2.map
AnnotationCryo-EM map of hamster prion 108-144 fibril, half map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster...

EntireName: 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster prion 108-144 fibril reveals an ordered water channel in the center
Components
  • Tissue: 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster prion 108-144 fibril reveals an ordered water channel in the center
    • Protein or peptide: Major prion protein
  • Ligand: water

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Supramolecule #1: 2.2 Angstrom cryo-EM tetra-protofilament structure of the hamster...

SupramoleculeName: 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 / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mesocricetus auratus (golden hamster) / Synthetically produced: Yes

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Macromolecule #1: Major prion protein

MacromoleculeName: Major prion protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Mesocricetus auratus (golden hamster)
Molecular weightTheoretical: 2.499955 KDa
SequenceString:
GAVVGGLGGY MLGSAMSRPM MHFGN

UniProtKB: Major prion protein

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 25 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 3.7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.77 Å
Applied symmetry - Helical parameters - Δ&Phi: -1.76 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 336759
Segment selectionNumber selected: 2368403 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: OTHER / Details: sinogram model
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 21.9
Output model

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

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