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8ty7

Crystal structure of 05.GC.w2.3C10 Fab in complex with H1 HA from A/California/04/2009(H1N1)

Method: X-RAY DIFFRACTION Dmax: 130.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemagglutinin

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

UniProt G8EHJ9

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 18–344 Fragment：HA1 subdomain (UNP residues 18-344) Hemagglutinin × 3 （I1ZFF9） GC_w2_3C10, heavy chain × 3 GC_w2_3C10, light chain × 3 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

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 8TY7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
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 construct Different oligomeric state Different ligand/ion 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
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 construct Different oligomeric state Different ligand/ion 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 construct 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 A； PDBConstruct 5–331； UniProt 18–344

Hemagglutinin

Influenza A virus (strain swl 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 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain B； UniProt 326–499 Fragment：HA2 subdomain (UNP residues 326-499) Hemagglutinin × 3 （G8EHJ9） GC_w2_3C10, heavy chain × 3 GC_w2_3C10, light chain × 3 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

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 8TY7 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
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 oligomeric state Different ligand/ion 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
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 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 B； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 8ty7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ty7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8ty7
Deposition date deposition_date2023-08-24
Structure title titleCrystal structure of 05.GC.w2.3C10 Fab in complex with H1 HA from A/California/04/2009(H1N1)
Keywords keywordsH1N1, Antibody, Hemagglutinin, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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_guinier39.57 Å
Radius of gyration Rg (electron density) rg_electron39.50 Å
Forward intensity I(0) i0165789000.00
Molecular weight molecular_weight102560.0 kDa
Excluded volume excluded_volume127590 ų
Envelope volume envelope_volume175710 ų
Hydration-shell volume shell_volume39244 ų
Envelope diameter envelope_diameter139.7 Å
Shell Rg shell_rg42.38 Å
Envelope Rg envelope_rg38.83 Å
Shape Rg shape_rg39.52 Å
Total Rg total_rg39.61 Å
Total atoms total_atoms7219
Residues n_residues926
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 dmax130.7 Å
Rg (real space) rg_real39.72 Å
Rg uncertainty (real space) rg_real_error1.28 Å
I(0) (real space) i0_real1.6580e+08
I(0) uncertainty (real space) i0_real_error2.8870e+06
Rg (reciprocal space) rg_reciprocal39.63 Å
I(0) (reciprocal space) i0_reciprocal165800000.0000
Solution quality estimate total_estimate0.8725
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.0 Å
Skewness Skewness skewness0.278
Kurtosis Kurtosis kurtosis-0.643
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12490000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.870; Smooth: 0.799
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)