SAXSdb — 7rk1

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

Capsid polyprotein VP70

Human astrovirus-8

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 429–647 Chain B； UniProt 429–647	Not recorded	scFv 3E8 × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295.15 K；0.2 M lithium citrate tribasic, 18 % PEG 3350	Resolution 2.05 Å R-free 0.238

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 7RK1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3QSQ Crystal structure of the projection domain of the human astrovirus capsid protein Deposited 2011-02-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 415–646（232 aa） Fragment：UNP residues 415-646	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.5；298 K；28% PEG 3000, 0.1 M CHES, 0.1 M glycine, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.215
5IBV Crystal Structure of Human Astrovirus capsid protein Deposited 2016-02-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 71–416（346 aa） Fragment：unp residues 71-416	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；VAPOR DIFFUSION, HANGING DROP, 0.2 M ammoium phosphate, 22% PEG 4000	Resolution 2.15 Å R-free 0.246
7RK2 Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv 2D9, an astrovirus-neutralizing antibody, at 2.65-A resolution Deposited 2021-07-21	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 429–647（219 aa） Chain B 429–647（219 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295.15 K；0.1 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 16 % PEG 10,000	Resolution 2.65 Å R-free 0.247
9WYD Crystal structure of HAstV8 spike and FcRn Deposited 2025-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 415–646（232 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；291.15 K；0.1 M BICINE pH 8.5, 8% w/v Polyethylene glycol monomethyl ether 5,000	Resolution 2.65 Å R-free 0.232
9WYG Crystal structure of HAstV8 spike Deposited 2025-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 415–646（232 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；291.15 K；0.1 M HEPES pH 7.5, 30% w/v Polyethylene glycol 1,000	Resolution 1.44 Å R-free 0.203
9WYG Crystal structure of HAstV8 spike Deposited 2025-09-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 415–646（232 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；291.15 K；0.1 M HEPES pH 7.5, 30% w/v Polyethylene glycol 1,000	Resolution 1.44 Å R-free 0.203

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

View Construct and Data Evidence

UniProt name	CAPSD_HASV8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–221； UniProt 429–647 Author chain B； PDBConstruct 3–221； UniProt 429–647

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	7rk1
Deposition date deposition_date	2021-07-21
Structure title title	Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv 3E8, an astrovirus-neutralizing antibody, at 2.05-A resolution
Keywords keywords	viral protein, capsid protein, icosahedral virus, single chain variable fragment; VIRAL PROTEIN
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	37.18 Å
Radius of gyration Rg (electron density) rg_electron	37.55 Å
Forward intensity I(0) i0	150475000.00
Molecular weight molecular_weight	99115.0 kDa
Excluded volume excluded_volume	123790 Å³
Envelope volume envelope_volume	155580 Å³
Hydration-shell volume shell_volume	38084 Å³
Envelope diameter envelope_diameter	138.9 Å
Shell Rg shell_rg	39.00 Å
Envelope Rg envelope_rg	37.81 Å
Shape Rg shape_rg	37.49 Å
Total Rg total_rg	37.81 Å
Total atoms total_atoms	7001
Residues n_residues	882
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	132.3 Å
Rg (real space) rg_real	37.67 Å
Rg uncertainty (real space) rg_real_error	1.44 Å
I(0) (real space) i0_real	1.5050e+08
I(0) uncertainty (real space) i0_real_error	2.5810e+06
Rg (reciprocal space) rg_reciprocal	37.37 Å
I(0) (reciprocal space) i0_reciprocal	150400000.0000
Solution quality estimate total_estimate	0.7926
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	129.2 Å
Skewness Skewness skewness	0.586
Kurtosis Kurtosis kurtosis	-0.329
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24880000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.631; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.487; Smooth: 0.920

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Capsid polyprotein VP70
Molecular weight formula_weight	25886.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7378

MGGEQFRVLLTVGPPMAPNTANSQNWVNKTIVPPENQYTVKIGIDLEHYTTMQGFTPVESVSWYTADFQPSDEPSPIPGLYARVNNTKKADVYGVQQFKSSHTNNRHQITSVFLVRVTTSFQVINYTSYFIRGAESGSNVSNLKIRDQTYHTPLQFTQGKWYLLTSTVMHDGPTSSGWVWMNQELTNNIAYRVDPGMMYLITPPPAASQLYFELHTVLPQAAAELALVPR

来源 Source

来源生物 organism	Human astrovirus-8
通用名 common_name	HAstV-8
NCBI Class编号 ncbi_taxonomy_id	43358
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	scFv 3E8
Molecular weight formula_weight	26878.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

DVQLQESGPGLVKPSQSLSLTCSVTGYSITSGYYWNWIRQFPGNKLEWMGYISYDGSNNYNPSLKNRISITRDTSKNQFFLKLNSVTTEDTATYYCATFYDGYDYWGQGTTLTVSSGGSGGGGSGGGGSGGGGSDIVMTQSHKFMSTSVGDRVSITCKASQDVSTAVAWYQQKPGQSPKLLIYWASTRHTGVPDRFTGSGSGTDYTLTISSVQAEDLALYYCQQHYSTPFTFGSGTKLEIKRASLVPR

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	335

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8. Citations (1)

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Unit-cell length a length_a	48.829 Å
Unit-cell length b length_b	80.429 Å
Unit-cell length c length_c	117.208 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	66.320 Å
R factor r_factor	0.2235
R_work r_work	0.2230
R_free r_free	0.2377

fit	/app/data/saxs_computation/rk/7rk1/7rk1.fit
pddf	/app/data/pr_computation/rk/7rk1/7rk1.pr.out
profile	/app/data/saxs_computation/rk/7rk1/7rk1.dat

Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv 3E8, an astrovirus-neutralizing antibody, at 2.05-A resolution

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

Capsid polyprotein VP70

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)