SAXSdb — 4yxl

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

Major prion protein

Mesocricetus auratus

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 90–232	Not recorded	No other associated polymer	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

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 4YXL	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 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 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 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 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
7LNA Infectious mammalian prion fibril (263K scrapie) Deposited 2021-02-06	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 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
7YAT CryoEM tetra protofilament structure of the hamster prion 108-144 fibril Deposited 2022-06-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 119–143（25 aa） Chain B 119–143（25 aa） Chain C 119–143（25 aa） Chain D 119–143（25 aa） Chain E 119–143（25 aa） Chain F 119–143（25 aa） Chain G 119–143（25 aa） Chain H 119–143（25 aa） Chain I 119–143（25 aa） Chain J 119–143（25 aa） Chain K 119–143（25 aa） Chain L 119–143（25 aa） Chain M 119–143（25 aa） Chain N 119–143（25 aa） Chain O 119–143（25 aa） Chain P 119–143（25 aa） Chain Q 119–143（25 aa） Chain R 119–143（25 aa） Chain S 119–143（25 aa） Chain T 119–143（25 aa） Chain U 119–143（25 aa） Chain V 119–143（25 aa） Chain X 119–143（25 aa） Chain Y 119–143（25 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 3.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 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 method 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 24–166； UniProt 90–232

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	4yxl
Deposition date deposition_date	2015-03-23
Structure title title	Crystal structure of Syrian hamster prion protein complexed with POM1 FAB
Keywords keywords	prion, antibody, Immune system complex, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	30.28 Å
Radius of gyration Rg (electron density) rg_electron	29.94 Å
Forward intensity I(0) i0	60730000.00
Molecular weight molecular_weight	59024.0 kDa
Excluded volume excluded_volume	72838 Å³
Envelope volume envelope_volume	98432 Å³
Hydration-shell volume shell_volume	29330 Å³
Envelope diameter envelope_diameter	104.6 Å
Shell Rg shell_rg	34.79 Å
Envelope Rg envelope_rg	29.99 Å
Shape Rg shape_rg	29.91 Å
Total Rg total_rg	30.46 Å
Total atoms total_atoms	4147
Residues n_residues	534
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	101.5 Å
Rg (real space) rg_real	30.53 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	6.0730e+07
I(0) uncertainty (real space) i0_real_error	9.7380e+05
Rg (reciprocal space) rg_reciprocal	30.42 Å
I(0) (reciprocal space) i0_reciprocal	60730000.0000
Solution quality estimate total_estimate	0.8480
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.2 Å
Skewness Skewness skewness	0.531
Kurtosis Kurtosis kurtosis	-0.278
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8437000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.824; Smooth: 0.703

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Major prion protein
Molecular weight formula_weight	18896.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4223

MGSSHHHHHHSSGLVPRGSHMLEGQGGGTHNQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPMMHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDIKIMERVVEQMCTTQYQKESQAYYDGRRSS

来源 Source

来源生物 organism	Mesocricetus auratus
通用名 common_name	Golden hamster
NCBI Class编号 ncbi_taxonomy_id	10036
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	POM1 FAB HEAVY CHAIN
Molecular weight formula_weight	23367.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQQSGTELVMPGASVKMSCKASGYTFTDYWMHWVKQRPGQGLEWIGSIDPSDSYTSHNEKFKGKATLTVDESSSTAYMQLSSLTSEDSAVYFCSRSGYGYYAMEYWGQGTSVTVSSAKTAPPSVYPLAPGGGATNSMVTLGCLVKGYFPEPVTVTWNSGSLSGGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	POM1 FAB LIGHT CHAIN
Molecular weight formula_weight	23509.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVLTQSPAILSVSPGERVSFSCRASQNIGTSIHWYQQRTNESPRLIIKYASESISGIPSRFSGSGSGTDFTLSINSVESEDIADYYCQQSNTWPYTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSETDQDSKDSTYSMSSTLTLTKDEYERHNTYTCEATHKTSTSPIVKSFNRNE

来源 Source

来源生物 organism	Mus musculus
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Mus musculus

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4yxlh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4yxlh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4yxll1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d4yxll2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (4 domains)

Domain ID domain_id	4yxlH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4yxlH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4yxlL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4yxlL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	83.916 Å
Unit-cell length b length_b	105.969 Å
Unit-cell length c length_c	76.326 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.604 Å
Low-resolution limit resolution_low	35.241 Å
R factor r_factor	0.2645
R_work r_work	0.2619
R_free r_free	0.3101

fit	/app/data/saxs_computation/yx/4yxl/4yxl.fit
pddf	/app/data/pr_computation/yx/4yxl/4yxl.pr.out
profile	/app/data/saxs_computation/yx/4yxl/4yxl.dat

Crystal structure of Syrian hamster prion protein complexed with POM1 FAB

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)