SAXSdb — 11ha

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

Major capsid protein VP1

Norovirus GII.4 Sydney 2012

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 221–530 Chain B； UniProt 221–530	Not recorded	24C10 Light Chain × 2 24C10 Heavy Chain × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；297.15 K；0.2 M HEPES: NaOH, pH 7.5, 8 % (w/v) PEG 8000, 8 % (v/v) Ethylene Glycol	Resolution 2.70 Å R-free 0.245

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 11HA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11HB Crystal structure of a GII.4 norovirus capsid P domain in complex with neutralizing antibody 17A5 Deposited 2026-02-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 221–530（310 aa） Chain E 221–530（310 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；297.15 K；0.1M Sodium Acetate, 2M Sodium formate	Resolution 3.36 Å R-free 0.300
11HB Crystal structure of a GII.4 norovirus capsid P domain in complex with neutralizing antibody 17A5 Deposited 2026-02-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 221–530（310 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；297.15 K；0.1M Sodium Acetate, 2M Sodium formate	Resolution 3.36 Å R-free 0.300

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A1P8DD09_NORV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–311； UniProt 221–530 Author chain B； PDBConstruct 2–311； UniProt 221–530

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	11ha
Deposition date deposition_date	2026-02-23
最后修订 last_revision	2026-05-27
Structure title title	Crystal structure of a GII.4 norovirus capsid P domain in complex with neutralizing antibody 24C10
Keywords keywords	Norovirus GII.4, P domain, Capsid protein, Antibody, VIRAL PROTEIN; 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	42.21 Å
Radius of gyration Rg (electron density) rg_electron	42.41 Å
Forward intensity I(0) i0	387045000.00
Molecular weight molecular_weight	158630.0 kDa
Excluded volume excluded_volume	197130 Å³
Envelope volume envelope_volume	259840 Å³
Hydration-shell volume shell_volume	53623 Å³
Envelope diameter envelope_diameter	140.9 Å
Shell Rg shell_rg	44.58 Å
Envelope Rg envelope_rg	42.76 Å
Shape Rg shape_rg	42.36 Å
Total Rg total_rg	42.66 Å
Total atoms total_atoms	11177
Residues n_residues	1451
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	138.2 Å
Rg (real space) rg_real	42.36 Å
Rg uncertainty (real space) rg_real_error	1.10 Å
I(0) (real space) i0_real	3.8700e+08
I(0) uncertainty (real space) i0_real_error	6.5600e+06
Rg (reciprocal space) rg_reciprocal	42.21 Å
I(0) (reciprocal space) i0_reciprocal	387000000.0000
Solution quality estimate total_estimate	0.8140
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	37.4 Å
Skewness Skewness skewness	0.370
Kurtosis Kurtosis kurtosis	-0.613
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	50490000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.000

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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	Major capsid protein VP1
Molecular weight formula_weight	34560.5 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	11185

GESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTTQLSPVNICNFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFVGKIQGMLTQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM

来源 Source

来源生物 organism	Norovirus GII.4 Sydney 2012
NCBI Class编号 ncbi_taxonomy_id	1776356
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	24C10 Light Chain
Molecular weight formula_weight	23352.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,K

QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKRWIYDTSKLASGVPARFSGSGSGTSYSLTISSMEAEDAATYYCQQWSSNPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

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 polymer

Description description	24C10 Heavy Chain
Molecular weight formula_weight	24661.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,G

QVQLQQSGAELMKPGASVKISCKATGYTFSSYWIEWVKQRPGHGLEWIGEILPGSGSTNYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARSWGFPYYAIDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRDCHHHHHH

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

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8. Citations (1)

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Unit-cell length a length_a	88.117 Å
Unit-cell length b length_b	56.428 Å
Unit-cell length c length_c	182.117 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.57 °
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	monoclinic

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	47.780 Å
R factor r_factor	0.2099
R_work r_work	0.2084
R_free r_free	0.2455

fit	/app/data/saxs_computation/1h/11ha/11ha.fit
pddf	/app/data/pr_computation/1h/11ha/11ha.pr.out
profile	/app/data/saxs_computation/1h/11ha/11ha.dat

Crystal structure of a GII.4 norovirus capsid P domain in complex with neutralizing antibody 24C10

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

Major capsid protein VP1

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 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)