SAXSdb — 7yat

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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 homooligomer Homooligomer Protein × 24 PDB declaration: 24-meric（24） Consistent with protein copy count	Chain A； UniProt 119–143 Chain B； UniProt 119–143 Chain C； UniProt 119–143 Chain D； UniProt 119–143 Chain E； UniProt 119–143 Chain F； UniProt 119–143 Chain G； UniProt 119–143 Chain H； UniProt 119–143 Chain I； UniProt 119–143 Chain J； UniProt 119–143 Chain K； UniProt 119–143 Chain L； UniProt 119–143 Chain M； UniProt 119–143 Chain N； UniProt 119–143 Chain O； UniProt 119–143 Chain P； UniProt 119–143 Chain Q； UniProt 119–143 Chain R； UniProt 119–143 Chain S； UniProt 119–143 Chain T； UniProt 119–143 Chain U； UniProt 119–143 Chain V； UniProt 119–143 Chain X； UniProt 119–143 Chain Y； UniProt 119–143	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 3.7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.20 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 7YAT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B10 SOLUTION NMR STRUCTURE OF RECOMBINANT SYRIAN HAMSTER PRION PROTEIN RPRP(90-231) , 25 STRUCTURES Deposited 1998-11-25	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 90–231（142 aa） Fragment：90 - 231	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；303 K；Pressure 1	Resolution not provided
2KKG NMR structure of the octarepeat region of prion protein bound to pentosan polysulfate Deposited 2009-06-19	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 23–106（84 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Pressure ambient NMR sample composition 0.5 mM [U-15N] octarepeats-1, 5 % [U-2H] D2O-2, 20 % [U-2H] DMSO-3, 20 mM pentosan polysulfate-4, 10 mM sodium acetate-5, 75 % H2O-6, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-13C; U-15N] octarepeats-7, 5 % [U-2H] D2O-8, 20 % [U-2H] DMSO-9, 20 mM pentosan polysulfate-10, 10 mM sodium acetate-11, 75 % H2O-12, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5 mM [U-13C; U-15N] octarepeats-13, 80 % [U-2H] D2O-14, 20 % [U-2H] DMSO-15, 20 mM pentosan polysulfate-16, 10 mM sodium acetate-17, 100% D2O \| 100% D2O	Resolution not provided
2LH8 Syrian hamster prion protein with thiamine Deposited 2011-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 125–228（104 aa） Fragment：UNP residues 125-228	Not recorded	VIB 3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM × 1	SOLUTION NMR NMR measurement conditions pH 6.2；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 0.3 mM [U-100% 15N] shPrP, 10 mM thiamine, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM shPrP, 12.5 mM thiamine, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM shPrP, 10 mM thiamine, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3NVE MMHFGN segment 138-143 from Syrian Hamster 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 × 12 PDB declaration: dodecameric	Chain A 138–143（6 aa） Chain B 138–143（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；1.2 M Ammonium sulfate, 200 mM BisTris pH 7.5, vapor diffusion, hanging drop, temperature 298K	Resolution 1.70 Å R-free 0.269
4YXL Crystal structure of Syrian hamster prion protein complexed with POM1 FAB Deposited 2015-03-23	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 90–232（143 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；25% PEG3350, 0.1 M BIS-TRIS, 0.2 M lithium sulphate	Resolution 2.60 Å R-free 0.310
7LNA Infectious mammalian prion fibril (263K scrapie) Deposited 2021-02-06	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 90–231（142 aa） Chain B 90–231（142 aa） Chain C 90–231（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
8WZX Cryo-EM structure of the hamster prion 23-144 fibril at pH 3.7 Deposited 2023-11-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 20 PDB declaration: eicosameric	Chain A 23–144（122 aa） Chain B 23–144（122 aa） Chain C 23–144（122 aa） Chain D 23–144（122 aa） Chain E 23–144（122 aa） Chain F 23–144（122 aa） Chain G 23–144（122 aa） Chain H 23–144（122 aa） Chain I 23–144（122 aa） Chain J 23–144（122 aa） Chain K 23–144（122 aa） Chain L 23–144（122 aa） Chain M 23–144（122 aa） Chain N 23–144（122 aa） Chain O 23–144（122 aa） Chain P 23–144（122 aa） Chain Q 23–144（122 aa） Chain R 23–144（122 aa） Chain S 23–144（122 aa） Chain T 23–144（122 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 3.7；20 mM NaOAc, 140 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRIO_MESAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–25； UniProt 119–143 Author chain B； PDBConstruct 1–25； UniProt 119–143 Author chain C； PDBConstruct 1–25； UniProt 119–143 Author chain D； PDBConstruct 1–25； UniProt 119–143 Author chain E； PDBConstruct 1–25； UniProt 119–143 Author chain F； PDBConstruct 1–25； UniProt 119–143 Author chain G； PDBConstruct 1–25； UniProt 119–143 Author chain H； PDBConstruct 1–25； UniProt 119–143 Author chain I； PDBConstruct 1–25； UniProt 119–143 Author chain J； PDBConstruct 1–25； UniProt 119–143 Author chain K； PDBConstruct 1–25； UniProt 119–143 Author chain L； PDBConstruct 1–25； UniProt 119–143 Author chain M； PDBConstruct 1–25； UniProt 119–143 Author chain N； PDBConstruct 1–25； UniProt 119–143 Author chain O； PDBConstruct 1–25； UniProt 119–143 Author chain P； PDBConstruct 1–25； UniProt 119–143 Author chain Q； PDBConstruct 1–25； UniProt 119–143 Author chain R； PDBConstruct 1–25； UniProt 119–143 Author chain S； PDBConstruct 1–25； UniProt 119–143 Author chain T； PDBConstruct 1–25； UniProt 119–143 Author chain U； PDBConstruct 1–25； UniProt 119–143 Author chain V； PDBConstruct 1–25； UniProt 119–143 Author chain X； PDBConstruct 1–25； UniProt 119–143 Author chain Y； PDBConstruct 1–25； UniProt 119–143

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7yat
Deposition date deposition_date	2022-06-28
Structure title title	CryoEM tetra protofilament structure of the hamster prion 108-144 fibril
Keywords keywords	Prion, fibril, hamster, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	24.51 Å
Radius of gyration Rg (electron density) rg_electron	23.01 Å
Forward intensity I(0) i0	64096600.00
Molecular weight molecular_weight	59567.0 kDa
Excluded volume excluded_volume	73265 Å³
Envelope volume envelope_volume	84189 Å³
Hydration-shell volume shell_volume	29409 Å³
Envelope diameter envelope_diameter	72.4 Å
Shell Rg shell_rg	30.94 Å
Envelope Rg envelope_rg	23.30 Å
Shape Rg shape_rg	23.01 Å
Total Rg total_rg	23.84 Å
Total atoms total_atoms	4104
Residues n_residues	600
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	71.0 Å
Rg (real space) rg_real	24.35 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	6.4100e+07
I(0) uncertainty (real space) i0_real_error	8.2170e+05
Rg (reciprocal space) rg_reciprocal	24.39 Å
I(0) (reciprocal space) i0_reciprocal	64100000.0000
Solution quality estimate total_estimate	0.8412
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.116
Kurtosis Kurtosis kurtosis	-0.632
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26850000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	2.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	336759

Description description	Major prion protein
Molecular weight formula_weight	2500.0 kDa
Source method src_method	syn
Copy count entity_count	24

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,X,Y
Atom count atom_count	4129

CryoEM tetra protofilament structure of the hamster prion 108-144 fibril

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

fit	/app/data/saxs_computation/ya/7yat/7yat.fit
pddf	/app/data/pr_computation/ya/7yat/7yat.pr.out
profile	/app/data/saxs_computation/ya/7yat/7yat.dat