SAXSdb — 9y41

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

Hemagglutinin

Influenza A 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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 63–285	Not recorded	Antibody 49_C09 heavy chain × 1 Antibody 49_C09 light chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Tris, pH 8.0, 65% (v/v) MPD	Resolution 2.89 Å R-free 0.283
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 63–285	Not recorded	Antibody 49_C09 heavy chain × 1 Antibody 49_C09 light chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Tris, pH 8.0, 65% (v/v) MPD	Resolution 2.89 Å R-free 0.283

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 9Y41	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9GSP Structure of uncleaved Influenza A/Victoria/2570/2019 Haemagglutinin. The 2021 Influenza A(H1N1)pdm09 egg-derived vaccine candidate. Deposited 2024-09-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–566（566 aa） Chain B 1–566（566 aa） Chain C 1–566（566 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 8；0.15 M NaCl, 25 mM Tris-HCl pH 8, and 0.1% beta-octylglucoside (BOG) cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.68 Å

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

View Construct and Data Evidence

UniProt name	A0A6M4YP75_9INFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–223； UniProt 63–285 Author chain G； PDBConstruct 1–223； UniProt 63–285

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	9y41
Deposition date deposition_date	2025-09-02
Structure title title	Crystal structure of hemagglutinin head domain from H1N1 Influenza A virus A/Victoria/2570/2019 bound to the 49_C09 antibody
Keywords keywords	Hemagglutinin, Head antibody, Influenza, Complex, ANTIVIRAL PROTEIN; ANTIVIRAL 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	45.41 Å
Radius of gyration Rg (electron density) rg_electron	46.57 Å
Forward intensity I(0) i0	301569000.00
Molecular weight molecular_weight	140970.0 kDa
Excluded volume excluded_volume	175790 Å³
Envelope volume envelope_volume	240720 Å³
Hydration-shell volume shell_volume	48974 Å³
Envelope diameter envelope_diameter	175.7 Å
Shell Rg shell_rg	43.10 Å
Envelope Rg envelope_rg	47.14 Å
Shape Rg shape_rg	46.50 Å
Total Rg total_rg	46.64 Å
Total atoms total_atoms	9937
Residues n_residues	1260
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	167.0 Å
Rg (real space) rg_real	46.27 Å
Rg uncertainty (real space) rg_real_error	2.21 Å
I(0) (real space) i0_real	3.0160e+08
I(0) uncertainty (real space) i0_real_error	6.2250e+06
Rg (reciprocal space) rg_reciprocal	45.41 Å
I(0) (reciprocal space) i0_reciprocal	301300000.0000
Solution quality estimate total_estimate	0.7215
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.2 Å
Skewness Skewness skewness	0.720
Kurtosis Kurtosis kurtosis	-0.021
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29820000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.513; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.330; Smooth: 0.507

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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	Hemagglutinin
Molecular weight formula_weight	25088.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,C
Atom count atom_count	9937

GVAPLHLGKCNIAGWILGNPECESLSTARSWSYIVETSNSDNGTCYPGDFINYEELREQLSSVSSFERFEIFPKTSSWPNHDSDNGVTAACPHAGAKSFYKNLIWLVKKGKSYPKINQTYINDKGKEVLVLWGIHHPPTIADQQSLYQNADAYVFVGTSRYSKKFKPEIATRPKVRDREGRMNYYWTLVEPGDKITFEATGNLVAPRYAFTMERDAGSGIIIS

来源 Source

来源生物 organism	Influenza A virus
NCBI Class编号 ncbi_taxonomy_id	11320
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Antibody 49_C09 heavy chain
Molecular weight formula_weight	24094.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QSTLKESGPTLVKPTETLTLTCTFSGFSLHTSGVGVGWIRQPPGKALECLALIYWNDDARYSPSLQSRLTITKDTSKNQVVLTMSNMDPVDTATYYCAHKGGGRDGYNSAAFDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Antibody 49_C09 light chain
Molecular weight formula_weight	22939.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SYVLTQPPSVSVAPGQTARIPCGGNNIGMKTVHWYQQRPGQAPVVVVYDDSRRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSVNHWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

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8. Citations (1)

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Unit-cell length a length_a	45.351 Å
Unit-cell length b length_b	256.212 Å
Unit-cell length c length_c	61.773 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.68 °
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	2.890 Å
Low-resolution limit resolution_low	36.660 Å
R factor r_factor	0.2378
R_work r_work	0.2340
R_free r_free	0.2828

fit	/app/data/saxs_computation/y4/9y41/9y41.fit
pddf	/app/data/pr_computation/y4/9y41/9y41.pr.out
profile	/app/data/saxs_computation/y4/9y41/9y41.dat

Crystal structure of hemagglutinin head domain from H1N1 Influenza A virus A/Victoria/2570/2019 bound to the 49_C09 antibody

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

Hemagglutinin

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)