SAXSdb — 1auy

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

TURNIP YELLOW MOSAIC VIRUS

Turnip yellow mosaic virus

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 × 180 PDB declaration: complete icosahedral assembly（180） Consistent with protein copy count	Chain A； UniProt 1–189 Chain B； UniProt 1–189 Chain C； UniProt 1–189	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；1.11 M AMMONIUM PHOSPHATE 100 MM MES PH 3.7 HANGING DROP, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.193
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–189 Chain B； UniProt 1–189 Chain C； UniProt 1–189	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；1.11 M AMMONIUM PHOSPHATE 100 MM MES PH 3.7 HANGING DROP, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.193
3	Protein homooligomer Homooligomer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain A； UniProt 1–189 Chain B； UniProt 1–189 Chain C； UniProt 1–189	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；1.11 M AMMONIUM PHOSPHATE 100 MM MES PH 3.7 HANGING DROP, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.193
4	Protein homooligomer Homooligomer Protein × 18 PDB declaration: octadecameric（18） Consistent with protein copy count	Chain A； UniProt 1–189 Chain B； UniProt 1–189 Chain C； UniProt 1–189	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；1.11 M AMMONIUM PHOSPHATE 100 MM MES PH 3.7 HANGING DROP, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.193
5	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–189 Chain B； UniProt 1–189 Chain C； UniProt 1–189	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；1.11 M AMMONIUM PHOSPHATE 100 MM MES PH 3.7 HANGING DROP, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.193
6	Protein homooligomer Homooligomer Protein × 45 PDB declaration: 45-meric（45） Consistent with protein copy count	Chain A； UniProt 1–189 Chain B； UniProt 1–189 Chain C； UniProt 1–189	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 3.7；1.11 M AMMONIUM PHOSPHATE 100 MM MES PH 3.7 HANGING DROP, vapor diffusion - hanging drop	Resolution 3.00 Å R-free 0.193

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 1AUY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W39 Crystal structure of an artificial top component of turnip yellow mosaic virus Deposited 2004-07-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 180 PDB declaration: 180-MERIC	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；1.16 M AMMONIUM PHOSPHATE PH 4.5, SITTING DROP	Resolution 3.75 Å R-free 0.251
1W39 Crystal structure of an artificial top component of turnip yellow mosaic virus Deposited 2004-07-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；1.16 M AMMONIUM PHOSPHATE PH 4.5, SITTING DROP	Resolution 3.75 Å R-free 0.251
1W39 Crystal structure of an artificial top component of turnip yellow mosaic virus Deposited 2004-07-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；1.16 M AMMONIUM PHOSPHATE PH 4.5, SITTING DROP	Resolution 3.75 Å R-free 0.251
1W39 Crystal structure of an artificial top component of turnip yellow mosaic virus Deposited 2004-07-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；1.16 M AMMONIUM PHOSPHATE PH 4.5, SITTING DROP	Resolution 3.75 Å R-free 0.251
1W39 Crystal structure of an artificial top component of turnip yellow mosaic virus Deposited 2004-07-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；1.16 M AMMONIUM PHOSPHATE PH 4.5, SITTING DROP	Resolution 3.75 Å R-free 0.251
1W39 Crystal structure of an artificial top component of turnip yellow mosaic virus Deposited 2004-07-14	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 15 PDB declaration: pentadecameric	Chain A 1–189（189 aa） Chain B 1–189（189 aa） Chain C 1–189（189 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；1.16 M AMMONIUM PHOSPHATE PH 4.5, SITTING DROP	Resolution 3.75 Å R-free 0.251

1 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COAT_TYMV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–190； UniProt 1–189 Author chain B； PDBConstruct 2–190； UniProt 1–189 Author chain C； PDBConstruct 2–190； UniProt 1–189

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	1auy
Deposition date deposition_date	1997-09-07
Structure title title	TURNIP YELLOW MOSAIC VIRUS
Keywords keywords	PLANT VIRUS, CAPSID PROTEIN, COAT PROTEIN, JELLYROLL, Icosahedral virus, Virus; VIRUS
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	29.75 Å
Radius of gyration Rg (electron density) rg_electron	29.45 Å
Forward intensity I(0) i0	48685300.00
Molecular weight molecular_weight	57654.0 kDa
Excluded volume excluded_volume	73365 Å³
Envelope volume envelope_volume	91070 Å³
Hydration-shell volume shell_volume	26899 Å³
Envelope diameter envelope_diameter	99.9 Å
Shell Rg shell_rg	35.03 Å
Envelope Rg envelope_rg	29.47 Å
Shape Rg shape_rg	29.44 Å
Total Rg total_rg	30.04 Å
Total atoms total_atoms	4045
Residues n_residues	541
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	95.1 Å
Rg (real space) rg_real	29.78 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	4.8690e+07
I(0) uncertainty (real space) i0_real_error	6.8540e+05
Rg (reciprocal space) rg_reciprocal	29.77 Å
I(0) (reciprocal space) i0_reciprocal	48680000.0000
Solution quality estimate total_estimate	0.8994
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.7 Å
Skewness Skewness skewness	0.239
Kurtosis Kurtosis kurtosis	-0.708
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6352000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.916

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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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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1auya_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.6 — Tymoviridae-like VP

Domain ID domain_id	d1auyb_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.6 — Tymoviridae-like VP

Domain ID domain_id	d1auyc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.6 — Tymoviridae-like VP

CATH v4.4 (3 domains)

Domain ID domain_id	1auyA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1auyB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1auyC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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8. Citations (2)

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Unit-cell length a length_a	515.500 Å
Unit-cell length b length_b	515.500 Å
Unit-cell length c length_c	309.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	540

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1870
R_work r_work	0.1870
R_free r_free	0.1930

Description description	TURNIP YELLOW MOSAIC VIRUS
Molecular weight formula_weight	20169.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4045

TURNIP YELLOW MOSAIC VIRUS

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

TURNIP YELLOW MOSAIC VIRUS

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Turnip yellow mosaic virus
NCBI Class编号 ncbi_taxonomy_id	12154
宿主生物 host_organism	Brassica rapa subsp. chinensis

fit	/app/data/saxs_computation/au/1auy/1auy.fit
pddf	/app/data/pr_computation/au/1auy/1auy.pr.out
profile	/app/data/saxs_computation/au/1auy/1auy.dat