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9ebc

H5N1 HA in complex with HC-5 Fab

Method: ELECTRON MICROSCOPY Dmax: 165.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemagglutinin HA1

Influenza A virus

UniProt A0AAX6NNG0

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 17–333 Chain C； UniProt 17–333 Chain E； UniProt 17–333 Not recorded Hemagglutinin HA2 × 3 （Q6DQ18） HC-5 Fab heavy chain × 3 HC-5 Fab light chain × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.87 Å

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 9EBC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9ZV0 CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H70 Deposited 2025-12-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–516（516 aa）
Chain B 1–516（516 aa）
Chain C 1–516（516 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.24 Å
9ZV1 CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H51 Deposited 2025-12-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–516（516 aa）
Chain B 1–516（516 aa）
Chain C 1–516（516 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9ZV4 CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H20 Deposited 2025-12-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–516（516 aa）
Chain B 1–516（516 aa）
Chain C 1–516（516 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.15 Å
9ZV9 CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H77 Deposited 2025-12-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–516（516 aa）
Chain B 1–516（516 aa）
Chain C 1–516（516 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.79 Å
9ZVH CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H33 Deposited 2025-12-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–516（516 aa）
Chain B 1–516（516 aa）
Chain C 1–516（516 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9ZVL CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H83 Deposited 2025-12-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–516（516 aa）
Chain B 1–516（516 aa）
Chain C 1–516（516 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0AAX6NNG0_9INFA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–317； UniProt 17–333 Author chain C； PDBConstruct 1–317； UniProt 17–333 Author chain E； PDBConstruct 1–317； UniProt 17–333

Hemagglutinin HA2

Influenza A virus

UniProt Q6DQ18

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 352–500 Chain D； UniProt 352–500 Chain F； UniProt 352–500 Fragment：UNP residues 345-506 Hemagglutinin HA1 × 3 （A0AAX6NNG0） HC-5 Fab heavy chain × 3 HC-5 Fab light chain × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.87 Å

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 9EBC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6CF5 Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in complex with small molecule N-Cyclohexyltaurine Deposited 2018-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 339–512（174 aa）
Chain D 339–512（174 aa）
Chain F 339–512（174 aa）
Not recorded NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PEG DI(HYDROXYETHYL)ETHER × 9 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；100 mM of CHES, pH 9.5 and 40% v/v PEG600, 20 degree celsiu
Resolution 2.04 Å R-free 0.222
6CFG Crystal structure of the A/Vietnam/1203/2004 (H5N1) influenza virus hemagglutinin in complex with small molecule JNJ4796 Deposited 2018-02-14 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 Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 339–512（174 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 EZ7 N-[2-(2-{4-[(R)-(2-methyl-2H-tetrazol-5-yl)(phenyl)methyl]piperazine-1-carbonyl}pyridin-4-yl)-1,3-benzoxazol-5-yl]acetamide × 3 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；0.2 M lithium sulfate, 20% w/v PEG3350
Resolution 2.32 Å R-free 0.241
6E7G Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus Deposited 2018-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 339–512（174 aa）
Chain D 339–512（174 aa）
Chain F 339–512（174 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；20% (w/v) PEG 3350, 0.1M Na-Acetate, pH 7.0.
Resolution 3.09 Å R-free 0.269
6E7H Crystal structure of H5 hemagglutinin mutant Y161A from A/Viet Nam/1203/2004 H5N1 influenza virus in complex with 3'-GcLN Deposited 2018-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 339–512（174 aa）
Chain D 339–512（174 aa）
Chain F 339–512（174 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；20% (w/v) PEG 3350, 0.1M Na-Acetate, pH 7.0.
Resolution 3.30 Å R-free 0.280

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HEMA_I02A6
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–149； UniProt 352–500 Author chain D； PDBConstruct 1–149； UniProt 352–500 Author chain F； PDBConstruct 1–149； UniProt 352–500

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 9ebc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ebc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ebc
Deposition date deposition_date2024-11-12
Structure title titleH5N1 HA in complex with HC-5 Fab
Keywords keywordsComplex, Viral, Antibody, Monoclonal, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier48.35 Å
Radius of gyration Rg (electron density) rg_electron48.01 Å
Forward intensity I(0) i0849654000.00
Molecular weight molecular_weight237810.0 kDa
Excluded volume excluded_volume295950 ų
Envelope volume envelope_volume390580 ų
Hydration-shell volume shell_volume70415 ų
Envelope diameter envelope_diameter162.4 Å
Shell Rg shell_rg48.24 Å
Envelope Rg envelope_rg48.37 Å
Shape Rg shape_rg48.00 Å
Total Rg total_rg48.05 Å
Total atoms total_atoms16740
Residues n_residues2115
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 dmax165.8 Å
Rg (real space) rg_real48.37 Å
Rg uncertainty (real space) rg_real_error1.54 Å
I(0) (real space) i0_real8.4970e+08
I(0) uncertainty (real space) i0_real_error1.6070e+07
Rg (reciprocal space) rg_reciprocal48.35 Å
I(0) (reciprocal space) i0_reciprocal849600000.0000
Solution quality estimate total_estimate0.8911
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary55.2 Å
Skewness Skewness skewness0.283
Kurtosis Kurtosis kurtosis-0.522
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha70310000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.941
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)