SAXSdb — 9zv4

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1. Structure Basics

entry_id	9zv4
deposition_date	2025-12-29
title	CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H20
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	45.33 Å
rg_electron	44.74 Å
i0	941955000.00
molecular_weight	248660.0 kDa
excluded_volume	308610 Å³
envelope_volume	417290 Å³
shell_volume	76029 Å³
envelope_diameter	141.9 Å
shell_rg	50.79 Å
envelope_rg	44.05 Å
shape_rg	44.74 Å
total_rg	44.97 Å
total_atoms	17483
n_residues	2133
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	144.1 Å
rg_real	45.19 Å
rg_real_error	1.36 Å
i0_real	9.4200e+08
i0_real_error	1.7750e+07
rg_reciprocal	45.33 Å
i0_reciprocal	942100000.0000
total_estimate	0.9012
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	53.5 Å
skewness	0.183
kurtosis	-0.617
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	79090000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.878

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Fab H20 Heavy Chain
formula_weight	26840.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,I,D
atom_count	17483

MGWSCIILFLVATATGVHSEVQLLESGGGLVQPGGSLRLSCAVSGFTFTNYAITWVRQAPGKGLEWVSVISGNGGSTYYVDSVKGRFTMSRDNSKKTVYLQMNSLRAEDTAVYYCAKDGPYFYYGMDVWGQGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKEPKSCDKTHHHHHHHH

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Fab H20 Light Chain
formula_weight	25612.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	L,K,G

MGWSCIILFLVATATGVHSDIQMTQSPSSLSASVGDRVTITCRTSQDIRSDLGWYQQKPGKAPKRLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCLQHNSFPMYTFGQGTKLDIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Hemagglutinin
formula_weight	65585.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C

MENIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPANDLCYPGSLNDYEELKHMLSRINHFEKIQIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISYNNTNREDLLILWGIHHSNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGQRGRMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNSPLRRRRRRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREGSSGSSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHHHHHGGSGLNDIFEAQKIEWHE

Source

organism	Influenza A virus
ncbi_taxonomy_id	11320
host_organism	Homo sapiens

Entity 4 branched

description	;N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1405.3 kDa
src_method	man
entity_count	3

Entity 5 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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resolution	3.150 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.15 Å
resolution_method	—
num_particles	118738

fit	/app/data/saxs_computation/zv/9zv4/9zv4.fit
pddf	/app/data/pr_computation/zv/9zv4/9zv4.pr.out
profile	/app/data/saxs_computation/zv/9zv4/9zv4.dat

CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H20

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)