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3qsq

Crystal structure of the projection domain of the human astrovirus capsid protein

Method: X-RAY DIFFRACTION Dmax: 58.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Capsid polyprotein

Human astrovirus 8

UniProt Q9IFX1

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 415–646 Fragment：UNP residues 415-646 No other associated polymer 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

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 3QSQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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
7RK1 Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv 3E8, an astrovirus-neutralizing antibody, at 2.05-A resolution Deposited 2021-07-21 Different construct Different mutation/modification Different oligomeric state 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；295.15 K；0.2 M lithium citrate tribasic, 18 % PEG 3350
Resolution 2.05 Å R-free 0.238
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 construct Different mutation/modification Different oligomeric state 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 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 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 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 2–233； UniProt 415–646

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3qsq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3qsq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3qsq
Deposition date deposition_date2011-02-21
Structure title titleCrystal structure of the projection domain of the human astrovirus capsid protein
Keywords keywordsreceptor binding domain, astrovirus capsid, Viral Protein; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.38 Å
Radius of gyration Rg (electron density) rg_electron16.89 Å
Forward intensity I(0) i010669000.00
Molecular weight molecular_weight24482.0 kDa
Excluded volume excluded_volume30692 ų
Envelope volume envelope_volume34828 ų
Hydration-shell volume shell_volume17192 ų
Envelope diameter envelope_diameter59.1 Å
Shell Rg shell_rg23.29 Å
Envelope Rg envelope_rg17.33 Å
Shape Rg shape_rg16.89 Å
Total Rg total_rg17.93 Å
Total atoms total_atoms1731
Residues n_residues216
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.4 Å
Rg (real space) rg_real18.28 Å
Rg uncertainty (real space) rg_real_error0.26 Å
I(0) (real space) i0_real1.0670e+07
I(0) uncertainty (real space) i0_real_error1.1320e+05
Rg (reciprocal space) rg_reciprocal18.29 Å
I(0) (reciprocal space) i0_reciprocal10670000.0000
Solution quality estimate total_estimate0.8939
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.7 Å
Skewness Skewness skewness0.173
Kurtosis Kurtosis kurtosis-0.338
Angular range angular_range— – 0.4350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2031000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.994
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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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9. Files and Curves (10)