SAXSdb — 9zvl

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1. Structure Basics

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

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	51.56 Å
rg_electron	51.27 Å
i0	929474000.00
molecular_weight	246810.0 kDa
excluded_volume	306330 Å³
envelope_volume	422660 Å³
shell_volume	72726 Å³
envelope_diameter	175.4 Å
shell_rg	49.05 Å
envelope_rg	51.25 Å
shape_rg	51.26 Å
total_rg	51.21 Å
total_atoms	17372
n_residues	2130
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	181.2 Å
rg_real	51.67 Å
rg_real_error	1.87 Å
i0_real	9.2950e+08
i0_real_error	1.8290e+07
rg_reciprocal	51.45 Å
i0_reciprocal	929200000.0000
total_estimate	0.8693
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.3 Å
skewness	0.360
kurtosis	-0.443
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	79670000.0000
n_real_points	32
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Hemagglutinin
formula_weight	65585.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	17372

MENIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPANDLCYPGSLNDYEELKHMLSRINHFEKIQIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISYNNTNREDLLILWGIHHSNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGQRGRMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNSPLRRRRRRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREGSSGSSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHHHGGSGLNDIFEAQKIEWHE

Source

organism	Influenza A virus
ncbi_taxonomy_id	11320
host_organism	Homo sapiens

Entity 2 polymer

description	Fab H83 Heavy Chain
formula_weight	28085.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,D,E

MGWSCIILFLVATATGVHSQEQLVESGGGVVQPGRSLRLSCTASGFTFSSHGMHWVRQAPGKGLEWIAVIWYDGTNKFYGDSVKGRFTISRDNSKNTLFLQMNSLRAEDTAVYYCARDRIQLWLQNYYHAMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKTVEPKSCDKTHHHHHHHH

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Fab H83 Light Chain
formula_weight	25432.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	L,F,G

MGWSCIILFLVATATGVHSDIQMTQSPSSLSASVGDRVTITCRASQNIRSYLNWYQQKPGKAPKFLIYGASSLQSGVPSRFSGSGSGTDFTLTISGLQPEDFATYYCQQSYTTLPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	12

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.480 Å
resolution_low	— Å
r_factor	—
r_work	—
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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)