SAXSdb — 9zvl

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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 × 9 PDB declaration: nonameric（9） Consistent with protein copy count	Chain A； UniProt 1–516 Chain B； UniProt 1–516 Chain C； UniProt 1–516	Not recorded	Fab H83 Heavy Chain × 3 Fab H83 Light Chain × 3 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

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 9ZVL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9EBC H5N1 HA in complex with HC-5 Fab Deposited 2024-11-12	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 17–333（317 aa） Chain C 17–333（317 aa） Chain E 17–333（317 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
9ZV0 CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H70 Deposited 2025-12-29	Different oligomeric state 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 oligomeric state 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 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	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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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

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 1–515； UniProt 1–516 Author chain B； PDBConstruct 1–515； UniProt 1–516 Author chain C； PDBConstruct 1–515； UniProt 1–516

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	9zvl
Deposition date deposition_date	2025-12-30
Structure title title	CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H83
Keywords keywords	H5N1, antibody, influenza, VIRAL PROTEIN, ANTIMICROBIAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	51.56 Å
Radius of gyration Rg (electron density) rg_electron	51.27 Å
Forward intensity I(0) i0	929474000.00
Molecular weight molecular_weight	246810.0 kDa
Excluded volume excluded_volume	306330 Å³
Envelope volume envelope_volume	422660 Å³
Hydration-shell volume shell_volume	72726 Å³
Envelope diameter envelope_diameter	175.4 Å
Shell Rg shell_rg	49.05 Å
Envelope Rg envelope_rg	51.25 Å
Shape Rg shape_rg	51.26 Å
Total Rg total_rg	51.21 Å
Total atoms total_atoms	17372
Residues n_residues	2130
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	181.2 Å
Rg (real space) rg_real	51.67 Å
Rg uncertainty (real space) rg_real_error	1.87 Å
I(0) (real space) i0_real	9.2950e+08
I(0) uncertainty (real space) i0_real_error	1.8290e+07
Rg (reciprocal space) rg_reciprocal	51.45 Å
I(0) (reciprocal space) i0_reciprocal	929200000.0000
Solution quality estimate total_estimate	0.8693
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	64.3 Å
Skewness Skewness skewness	0.360
Kurtosis Kurtosis kurtosis	-0.443
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	79670000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.908; Smooth: 0.895

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin
Molecular weight formula_weight	65585.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	17372

MENIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPANDLCYPGSLNDYEELKHMLSRINHFEKIQIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISYNNTNREDLLILWGIHHSNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGQRGRMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNSPLRRRRRRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREGSSGSSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHHHGGSGLNDIFEAQKIEWHE

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Fab H83 Heavy Chain
Molecular weight formula_weight	28085.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,D,E

MGWSCIILFLVATATGVHSQEQLVESGGGVVQPGRSLRLSCTASGFTFSSHGMHWVRQAPGKGLEWIAVIWYDGTNKFYGDSVKGRFTISRDNSKNTLFLQMNSLRAEDTAVYYCARDRIQLWLQNYYHAMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKTVEPKSCDKTHHHHHHHH

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Fab H83 Light Chain
Molecular weight formula_weight	25432.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,F,G

MGWSCIILFLVATATGVHSDIQMTQSPSSLSASVGDRVTITCRASQNIRSYLNWYQQKPGKAPKFLIYGASSLQSGVPSRFSGSGSGTDFTLTISGLQPEDFATYYCQQSYTTLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 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	12

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

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

Resolution resolution	3.480 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/zv/9zvl/9zvl.fit
pddf	/app/data/pr_computation/zv/9zvl/9zvl.pr.out
profile	/app/data/saxs_computation/zv/9zvl/9zvl.dat

CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H83

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

6. Entities and Polymers Entities & Polymers (4)

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 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)