SAXSdb — 9y3x

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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 E； UniProt 18–340	Not recorded	Hemagglutinin × 1 （I1ZFF9） Antibody 3_H2 heavy chain × 1 Antibody 3_H2 light 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；0.2M Tri-potassium citrate, 20% (w/v) PEG3350, pH 8.3	Resolution 3.39 Å R-free 0.261

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 9Y3X	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
9Y3Y Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 49_C09 antibody Deposited 2025-09-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 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；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
9Y3Y Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 49_C09 antibody Deposited 2025-09-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 18–340（323 aa）	Not recorded	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

2 other PDB entries and 3 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 E； 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 F； UniProt 326–499	Fragment：HA2 subdomain (UNP residues 326-499)	Hemagglutinin × 1 （G8EHJ9） Antibody 3_H2 heavy chain × 1 Antibody 3_H2 light 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；0.2M Tri-potassium citrate, 20% (w/v) PEG3350, pH 8.3	Resolution 3.39 Å R-free 0.261

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 9Y3X	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
9Y3Y Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 49_C09 antibody Deposited 2025-09-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 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；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
9Y3Y Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 49_C09 antibody Deposited 2025-09-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 326–499（174 aa） Fragment：HA2 subdomain (UNP residues 326-499)	Not recorded	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

3 other PDB entries and 4 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 F； 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	9y3x
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 3_H2 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	49.51 Å
Radius of gyration Rg (electron density) rg_electron	51.16 Å
Forward intensity I(0) i0	163751000.00
Molecular weight molecular_weight	103300.0 kDa
Excluded volume excluded_volume	128720 Å³
Envelope volume envelope_volume	185750 Å³
Hydration-shell volume shell_volume	36322 Å³
Envelope diameter envelope_diameter	188.6 Å
Shell Rg shell_rg	42.73 Å
Envelope Rg envelope_rg	51.65 Å
Shape Rg shape_rg	51.15 Å
Total Rg total_rg	50.82 Å
Total atoms total_atoms	7271
Residues n_residues	911
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	180.2 Å
Rg (real space) rg_real	51.20 Å
Rg uncertainty (real space) rg_real_error	2.85 Å
I(0) (real space) i0_real	1.6380e+08
I(0) uncertainty (real space) i0_real_error	3.7040e+06
Rg (reciprocal space) rg_reciprocal	49.53 Å
I(0) (reciprocal space) i0_reciprocal	163400000.0000
Solution quality estimate total_estimate	0.6253
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.723
Kurtosis Kurtosis kurtosis	-0.240
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6575000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.273; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.096; Smooth: 0.211

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin
Molecular weight formula_weight	36243.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E
Atom count atom_count	7271

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

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 3_H2 heavy chain
Molecular weight formula_weight	24185.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QGTLKESGPAMVKPTQTLTLTCTFSGFSLDTSGMCVAWIRQPPGKALEWLALFDWDNNKYYSPSLKTRLNMSKGRSRNQVVLTMTNMDPVDTGTYYCARKVYGSFYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

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 3_H2 light chain
Molecular weight formula_weight	23573.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVLTQSPATLSLSPGDSATLSCRASQDVSANLAWYQQKPGQAPRLVIYDATNRATGIPARFSGSGLGTDFTLTISSLEPEDFAVYYCQQRSNWPPVYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	130.894 Å
Unit-cell length b length_b	130.894 Å
Unit-cell length c length_c	142.840 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	6

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

Resolution resolution	3.390 Å
Low-resolution limit resolution_low	48.250 Å
R factor r_factor	0.2099
R_work r_work	0.2043
R_free r_free	0.2608

fit	/app/data/saxs_computation/y3/9y3x/9y3x.fit
pddf	/app/data/pr_computation/y3/9y3x/9y3x.pr.out
profile	/app/data/saxs_computation/y3/9y3x/9y3x.dat

Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 3_H2 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 (6)

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 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)