SAXSdb — 7rvd

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Major prion protein

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 167–175	Fragment：UNP residues 167-175	No other associated polymer	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

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 7RVD	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 method 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
7TD6 aRML prion fibril Deposited 2021-12-30	Different construct Different mutation/modification Different oligomeric state Different experimental method 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 method 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
8DJA Cryo-EM structure of mouse PrP23-144 amyloid fibrils (polymorph 1) Deposited 2022-06-30	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric	Chain A 23–143（121 aa） Chain B 23–143（121 aa） Chain C 23–143（121 aa） Chain D 23–143（121 aa） Chain E 23–143（121 aa） Chain F 23–143（121 aa） Chain G 23–143（121 aa） Chain H 23–143（121 aa） Chain I 23–143（121 aa） Chain J 23–143（121 aa） Chain K 23–143（121 aa） Chain L 23–143（121 aa） Chain M 23–143（121 aa） Chain N 23–143（121 aa） Chain O 23–143（121 aa） Chain P 23–143（121 aa） Chain Q 23–143（121 aa） Chain R 23–143（121 aa） Chain S 23–143（121 aa） Chain T 23–143（121 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.92 Å
8EFU a22L prion fibril Deposited 2022-09-09	Different construct Different mutation/modification Different oligomeric state Different experimental method 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 1–9； UniProt 167–175

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7rvd
Deposition date deposition_date	2021-08-18
Structure title title	Segment from the mouse/cow prion protein 168-176 QYSNQNNFV
Keywords keywords	amyloid, prion, fibril, mouse, cow, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method method	ELECTRON CRYSTALLOGRAPHY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	9.42 Å
Radius of gyration Rg (electron density) rg_electron	9.03 Å
Forward intensity I(0) i0	57554.40
Molecular weight molecular_weight	1113.0 kDa
Excluded volume excluded_volume	1331 Å³
Envelope volume envelope_volume	1797 Å³
Hydration-shell volume shell_volume	2408 Å³
Envelope diameter envelope_diameter	32.0 Å
Shell Rg shell_rg	11.64 Å
Envelope Rg envelope_rg	9.57 Å
Shape Rg shape_rg	8.96 Å
Total Rg total_rg	10.24 Å
Total atoms total_atoms	147
Residues n_residues	9
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	36.6 Å
Rg (real space) rg_real	9.67 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	5.7550e+04
I(0) uncertainty (real space) i0_real_error	6.1500e+02
Rg (reciprocal space) rg_reciprocal	9.66 Å
I(0) (reciprocal space) i0_reciprocal	57550.0000
Solution quality estimate total_estimate	0.7364
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.7 Å
Skewness Skewness skewness	0.733
Kurtosis Kurtosis kurtosis	0.147
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3897.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.520; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.086; Smooth: 0.925

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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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Unit-cell length a length_a	4.870 Å
Unit-cell length b length_b	10.170 Å
Unit-cell length c length_c	31.290 Å
Unit-cell angle α angle_alpha	94.65 °
Unit-cell angle β angle_beta	90.73 °
Unit-cell angle γ angle_gamma	101.15 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.003 Å
Low-resolution limit resolution_low	10.391 Å
R factor r_factor	0.2056
R_work r_work	0.2011
R_free r_free	0.2499

Resolution resolution	1.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	—

Description description	Major prion protein
Molecular weight formula_weight	1113.1 kDa
Source method src_method	syn
Copy count entity_count	1

Segment from the mouse/cow prion protein 168-176 QYSNQNNFV

1. Protein Identity and Related Structures Protein Identity & Related Structures

Major prion protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	147

fit	/app/data/saxs_computation/rv/7rvd/7rvd.fit
pddf	/app/data/pr_computation/rv/7rvd/7rvd.pr.out
profile	/app/data/saxs_computation/rv/7rvd/7rvd.dat