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8dja

Cryo-EM structure of mouse PrP23-144 amyloid fibrils (polymorph 1)

Method: ELECTRON MICROSCOPY Dmax: 99.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Major prion protein

Mus musculus

UniProt P04925

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 20 PDB declaration: eicosameric（20） Consistent with protein copy count Chain A； UniProt 23–143 Chain B； UniProt 23–143 Chain C； UniProt 23–143 Chain D； UniProt 23–143 Chain E； UniProt 23–143 Chain F； UniProt 23–143 Chain G； UniProt 23–143 Chain H； UniProt 23–143 Chain I； UniProt 23–143 Chain J； UniProt 23–143 Chain K； UniProt 23–143 Chain L； UniProt 23–143 Chain M； UniProt 23–143 Chain N； UniProt 23–143 Chain O； UniProt 23–143 Chain P； UniProt 23–143 Chain Q； UniProt 23–143 Chain R； UniProt 23–143 Chain S； UniProt 23–143 Chain T； UniProt 23–143 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 6.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.92 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8DJA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AG2 PRION PROTEIN DOMAIN PRP(121-231) FROM MOUSE, NMR, 2 MINIMIZED AVERAGE STRUCTURE Deposited 1997-03-31 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 123–225（103 aa） Fragment：DOMAIN 121 - 231
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；293 K
Resolution not provided
1XYX mouse prion protein fragment 121-231 Deposited 2004-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 120–231（112 aa） Fragment：C-terminal domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；293 K；Ionic strength (raw mmCIF value) 10；Pressure ambient
NMR sample composition 1mM mPrP(121-231) U-15N,13C; 10mM acetate | 90% H2O/10% D2O
Resolution not provided
1Y15 Mouse Prion Protein with mutation N174T Deposited 2004-11-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 120–231（112 aa） Fragment：C-terminal domain
Mutation：N174T No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；293 K；Ionic strength (raw mmCIF value) 10；Pressure ambient
NMR sample composition 1mM mPrP(121-231) U-15N,13C; 10mM acetate | 90% H2O/10% D2O
Resolution not provided
1Y16 mouse prion protein with mutations S170N and N174T Deposited 2004-11-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 120–231（112 aa） Fragment：C-terminal domain
Mutation：S170N, N174T No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；293 K；Ionic strength (raw mmCIF value) 10；Pressure ambient
NMR sample composition 1mM mprp(121-213) S170N,N174T U-15N,13C;10mM acetate | 90% H2O/10% D2O
Resolution not provided
2K5O Mouse Prion Protein (121-231) with Mutation S170N Deposited 2008-06-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 120–231（112 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；298.2 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 0.4mM [U-99% 13C; U-99% 15N] Prion Protein, 10% D2O, 90% H2O, 10mM [U-2H] sodium acetate, 0.02% sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KFM Mouse Prion Protein (121-231) with Mutations Y225A and Y226A Deposited 2009-02-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 120–231（112 aa）
Mutation：Y225A,Y226A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；293.1 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 10 mM [U-100% 2H] sodium acetate-1, 2 mM [U-99% 13C; U-99% 15N] entity-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KFO Mouse Prion Protein (121-231) with Mutation V166A Deposited 2009-02-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 120–231（112 aa）
Mutation：V166A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.5；293.1 K；Ionic strength (raw mmCIF value) 0.01；Pressure ambient
NMR sample composition 1.4 mM [U-99% 13C; U-99% 15N] protein, 10 mM [U-100% 2H] sodium acetate, 0.02 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KU5 Mouse Prion Protein (121-231) with mutation D167S Deposited 2010-02-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 120–231（112 aa） Fragment：UNP residues 119-231
Mutation：D167S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 10；298 K；Pressure ambient
NMR sample composition 10 mM [U-2H] sodium acetate-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2KU6 Mouse Prion Protein (121-231) with mutations D167S and N173K Deposited 2010-02-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 120–231（112 aa） Fragment：UNP residues 119-231
Mutation：D167S, N173K No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 10；298 K；Pressure ambient
NMR sample composition 10 mM [U-2H] sodium acetate-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3NVG MIHFGN segment 137-142 from mouse prion Deposited 2010-07-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 137–142（6 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM HEPES 7.5, vapor diffusion, hanging drop, temperature 298K
Resolution 1.48 Å R-free 0.205
3NVH MIHFGND segment 137-143 from mouse prion Deposited 2010-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric
Chain A 137–143（7 aa）
Not recorded TFA trifluoroacetic acid × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100mM HEPES ph 7.0, 10% PEG 1200, vapor diffusion, hanging drop, temperature 298K
Resolution 1.61 Å R-free 0.197
4H88 Structure of POM1 FAB fragment complexed with mouse PrPc Fragment 120-230 Deposited 2012-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 120–230（111 aa） Fragment：C-TERM FRAGMENT
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25% PEG3350, 0.1 M BIS-TRIS, 0.2 M lithium sulphate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.90 Å R-free 0.234
4J8R Structure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody fragment Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 67–82（16 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；28% PEG 1000, 0.1M HEPES, 0.2M Calcium Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.257
4J8R Structure of an octapeptide repeat of the prion protein bound to the POM2 Fab antibody fragment Deposited 2013-02-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 67–82（16 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；28% PEG 1000, 0.1M HEPES, 0.2M Calcium Chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.30 Å R-free 0.257
4MA7 Crystal structure of mouse prion protein complexed with Promazine Deposited 2013-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 116–229（114 aa） Fragment：UNP residues 116-229
Not recorded P2Z Promazine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25% PEG3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.97 Å R-free 0.247
4MA8 Crystal structure of mouse prion protein complexed with Chlorpromazine Deposited 2013-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 116–229（114 aa） Fragment：UNP residues 116-229
Not recorded Z80 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；25% PEG3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.20 Å R-free 0.236
6AQ7 Structure of POM6 FAB fragment complexed with mouse PrPc Deposited 2017-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 127–225（99 aa） Fragment：UNP residues 127-225
Not recorded GOL GLYCEROL × 2 TCE 3,3',3''-phosphanetriyltripropanoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M Sodium malonate pH 7.0, 12% PEG8000 along with 5mM TCEP, 5mM Praseodymium acetate and ethanol
Resolution 1.83 Å R-free 0.230
6HER Mouse prion protein in complex with Nanobody 484 Deposited 2018-08-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 117–226（110 aa）
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris pH 8, 1.5 M ammonium sulfate
Resolution 1.20 Å R-free 0.195
6HHD Mouse Prion Protein in complex with Nanobody 484 Deposited 2018-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 118–225（108 aa）
Chain C 118–224（107 aa）
Not recorded CL CHLORIDE ION × 3 SO4 SULFATE ION × 4 GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.15 M ammonium sulfate, 0.1 M MES pH6.0, 15% w/v PEG 40000.
Resolution 2.10 Å R-free 0.245
7QIG Infectious mouse-adapted RML scrapie prion fibril purified from terminally-infected mouse brains Deposited 2021-12-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 94–225（132 aa）
Chain B 94–225（132 aa）
Chain C 94–225（132 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7RVD Segment from the mouse/cow prion protein 168-176 QYSNQNNFV Deposited 2021-08-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 167–175（9 aa） Fragment：UNP residues 167-175
Not recorded No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；0.5 M zinc acetate, 15% ethanol, 0.2 M MES, pH 6
Resolution 1.00 Å R-free 0.250
7TD6 aRML prion fibril Deposited 2021-12-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain 1 1–254（254 aa）
Chain A 1–254（254 aa）
Chain B 1–254（254 aa）
Chain C 1–254（254 aa）
Chain D 1–254（254 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8A00 Infectious mouse-adapted ME7 scrapie prion fibril purified from terminally-infected mouse brains Deposited 2022-05-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 94–229（136 aa）
Chain B 94–229（136 aa）
Chain C 94–229（136 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8EFU a22L prion fibril Deposited 2022-09-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–231（231 aa）
Chain B 1–231（231 aa）
Chain C 1–231（231 aa）
Chain D 1–231（231 aa）
Chain E 1–231（231 aa）
Mutation：S233Stop Mutation：S233Stop Mutation：S233Stop Mutation：S233Stop Mutation：S233Stop No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Sample suspended in 20 mM Tris pH 7.4, 100 mM containing 0.02% amphipol 8-35
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å

23 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRIO_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–123； UniProt 23–143 Author chain B； PDBConstruct 3–123； UniProt 23–143 Author chain C； PDBConstruct 3–123； UniProt 23–143 Author chain D； PDBConstruct 3–123； UniProt 23–143 Author chain E； PDBConstruct 3–123； UniProt 23–143 Author chain F； PDBConstruct 3–123； UniProt 23–143 Author chain G； PDBConstruct 3–123； UniProt 23–143 Author chain H； PDBConstruct 3–123； UniProt 23–143 Author chain I； PDBConstruct 3–123； UniProt 23–143 Author chain J； PDBConstruct 3–123； UniProt 23–143 Author chain K； PDBConstruct 3–123； UniProt 23–143 Author chain L； PDBConstruct 3–123； UniProt 23–143 Author chain M； PDBConstruct 3–123； UniProt 23–143 Author chain N； PDBConstruct 3–123； UniProt 23–143 Author chain O； PDBConstruct 3–123； UniProt 23–143 Author chain P； PDBConstruct 3–123； UniProt 23–143 Author chain Q； PDBConstruct 3–123； UniProt 23–143 Author chain R； PDBConstruct 3–123； UniProt 23–143 Author chain S； PDBConstruct 3–123； UniProt 23–143 Author chain T； PDBConstruct 3–123； UniProt 23–143

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 8dja

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8dja
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8dja
Deposition date deposition_date2022-06-30
Structure title titleCryo-EM structure of mouse PrP23-144 amyloid fibrils (polymorph 1)
Keywords keywordsmoPrP23-144, amyloid, prion diseases, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.52 Å
Radius of gyration Rg (electron density) rg_electron30.06 Å
Forward intensity I(0) i071167100.00
Molecular weight molecular_weight65959.0 kDa
Excluded volume excluded_volume82675 ų
Envelope volume envelope_volume109040 ų
Hydration-shell volume shell_volume31205 ų
Envelope diameter envelope_diameter98.0 Å
Shell Rg shell_rg36.24 Å
Envelope Rg envelope_rg30.09 Å
Shape Rg shape_rg30.02 Å
Total Rg total_rg30.79 Å
Total atoms total_atoms4600
Residues n_residues680
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax99.5 Å
Rg (real space) rg_real30.60 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real7.1170e+07
I(0) uncertainty (real space) i0_real_error1.0580e+06
Rg (reciprocal space) rg_reciprocal30.57 Å
I(0) (reciprocal space) i0_reciprocal71170000.0000
Solution quality estimate total_estimate0.8926
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.4 Å
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.527
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14310000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.913; Smooth: 0.928
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)