SAXSdb — 9y3y

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

Hemagglutinin

Influenza A virus (A/California/04/2009(H1N1))

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 18–340	Not recorded	Hemagglutinin × 1 （I1ZFF9） Antibody 49_C09 light chain × 1 Antibody 49_C09 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；2M ammonium sulfate, 15% (v/v) ethylene glycol, 0.2M lithium sulfate, 0.1M CAPS, pH 10.5	Resolution 3.80 Å R-free 0.240
2	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 18–340	Not recorded	Hemagglutinin × 1 （I1ZFF9） Antibody 49_C09 light chain × 1 Antibody 49_C09 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；2M ammonium sulfate, 15% (v/v) ethylene glycol, 0.2M lithium sulfate, 0.1M CAPS, pH 10.5	Resolution 3.80 Å R-free 0.240

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 9Y3Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8TY7 Crystal structure of 05.GC.w2.3C10 Fab in complex with H1 HA from A/California/04/2009(H1N1) Deposited 2023-08-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 18–344（327 aa） Fragment：HA1 subdomain (UNP residues 18-344)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium acetate, pH 6.4, 18% PEG3350	Resolution 3.21 Å R-free 0.288
9Y3X Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 3_H2 antibody Deposited 2025-09-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 18–340（323 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Tri-potassium citrate, 20% (w/v) PEG3350, pH 8.3	Resolution 3.39 Å R-free 0.261

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

View Construct and Data Evidence

UniProt name	G8EHJ9_I09A0
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–327； UniProt 18–340 Author chain C； PDBConstruct 5–327； UniProt 18–340

Hemagglutinin

Influenza A virus (A/California/04/2009(H1N1))

UniProt I1ZFF9

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 326–499	Fragment：HA2 subdomain (UNP residues 326-499)	Hemagglutinin × 1 （G8EHJ9） Antibody 49_C09 light chain × 1 Antibody 49_C09 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；2M ammonium sulfate, 15% (v/v) ethylene glycol, 0.2M lithium sulfate, 0.1M CAPS, pH 10.5	Resolution 3.80 Å R-free 0.240
2	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 326–499	Fragment：HA2 subdomain (UNP residues 326-499)	Hemagglutinin × 1 （G8EHJ9） Antibody 49_C09 light chain × 1 Antibody 49_C09 heavy chain × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；2M ammonium sulfate, 15% (v/v) ethylene glycol, 0.2M lithium sulfate, 0.1M CAPS, pH 10.5	Resolution 3.80 Å R-free 0.240

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 9Y3Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8TXP Crystal structure of 05.GC.w13.01 Fab in complex with H1 HA from A/California/04/2009(H1N1) Deposited 2023-08-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 326–499（174 aa） Fragment：HA2 subdomain (UNP residues 326-499)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium acetate, pH 6.2, 20% PEG3350	Resolution 2.75 Å R-free 0.292
8TY7 Crystal structure of 05.GC.w2.3C10 Fab in complex with H1 HA from A/California/04/2009(H1N1) Deposited 2023-08-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 326–499（174 aa） Fragment：HA2 subdomain (UNP residues 326-499)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M sodium acetate, pH 6.4, 18% PEG3350	Resolution 3.21 Å R-free 0.288
9Y3X Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 3_H2 antibody Deposited 2025-09-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 326–499（174 aa） Fragment：HA2 subdomain (UNP residues 326-499)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Tri-potassium citrate, 20% (w/v) PEG3350, pH 8.3	Resolution 3.39 Å R-free 0.261

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	I1ZFF9_9INFA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–174； UniProt 326–499 Author chain D； PDBConstruct 1–174； UniProt 326–499

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	9y3y
Deposition date deposition_date	2025-09-02
Structure title title	Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 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	76.33 Å
Radius of gyration Rg (electron density) rg_electron	77.44 Å
Forward intensity I(0) i0	610768000.00
Molecular weight molecular_weight	205160.0 kDa
Excluded volume excluded_volume	255370 Å³
Envelope volume envelope_volume	461490 Å³
Hydration-shell volume shell_volume	56350 Å³
Envelope diameter envelope_diameter	290.2 Å
Shell Rg shell_rg	65.57 Å
Envelope Rg envelope_rg	74.62 Å
Shape Rg shape_rg	77.43 Å
Total Rg total_rg	77.24 Å
Total atoms total_atoms	14445
Residues n_residues	1812
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	230.8 Å
Rg (real space) rg_real	74.44 Å
Rg uncertainty (real space) rg_real_error	1.70 Å
I(0) (real space) i0_real	6.0320e+08
I(0) uncertainty (real space) i0_real_error	1.3510e+07
Rg (reciprocal space) rg_reciprocal	72.83 Å
I(0) (reciprocal space) i0_reciprocal	605300000.0000
Solution quality estimate total_estimate	0.8090
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	92.3 Å
Skewness Skewness skewness	0.405
Kurtosis Kurtosis kurtosis	-0.468
Angular range angular_range	— – 0.1000 Å⁻¹
Current regularization parameter α current_alpha	0.0474
Highest regularization parameter α highest_alpha	12180000.0000
Real-space data points n_real_points	21
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.746; Stabil: 0.983; Sysdev: 1.000; Positv: 1.000; Valcen: 0.853; Smooth: 0.386

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin
Molecular weight formula_weight	36243.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,A
Atom count atom_count	14461

ADPGDTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPS

来源 Source

来源生物 organism	Influenza A virus (A/California/04/2009(H1N1))
NCBI Class编号 ncbi_taxonomy_id	641501
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Hemagglutinin
Molecular weight formula_weight	20206.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDSGR

来源 Source

来源生物 organism	Influenza A virus (A/California/04/2009(H1N1))
NCBI Class编号 ncbi_taxonomy_id	641501
宿主生物 host_organism	Trichoplusia ni

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,F

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

Entity 4 Entity 4 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,E

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 5 Entity 5 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	166.919 Å
Unit-cell length b length_b	166.919 Å
Unit-cell length c length_c	347.947 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	12

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	49.710 Å
R factor r_factor	0.2067
R_work r_work	0.2051
R_free r_free	0.2400

fit	/app/data/saxs_computation/y3/9y3y/9y3y.fit
pddf	/app/data/pr_computation/y3/9y3y/9y3y.pr.out
profile	/app/data/saxs_computation/y3/9y3y/9y3y.dat

Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 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

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 (7)

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

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)