SAXSdb — 9zvh

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1. Structure Basics

entry_id	9zvh
deposition_date	2025-12-30
title	CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H33
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	46.81 Å
rg_electron	46.00 Å
i0	914103000.00
molecular_weight	243760.0 kDa
excluded_volume	301830 Å³
envelope_volume	409830 Å³
shell_volume	73568 Å³
envelope_diameter	145.8 Å
shell_rg	50.84 Å
envelope_rg	45.59 Å
shape_rg	46.00 Å
total_rg	46.18 Å
total_atoms	17141
n_residues	2100
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	143.8 Å
rg_real	46.56 Å
rg_real_error	0.97 Å
i0_real	9.1410e+08
i0_real_error	1.5560e+07
rg_reciprocal	46.81 Å
i0_reciprocal	914400000.0000
total_estimate	0.8980
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	67.7 Å
skewness	0.058
kurtosis	-0.687
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	88140000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.783

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	H33 Fab Heavy Chain
formula_weight	13099.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,I,D
atom_count	17141

QVLLVQSGAEMKRPGASVKVSCTASGYTFTNYDIHWVRQASGQGLEWMGWMNPNSGDTGYAQKFQGRVTLTRDTSINTAYMELRRLNSEDTAVYYCARGGVSYNFDHWGQGTLVTVSS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Fab H33 Light Chain
formula_weight	11728.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	L,K,G

DIQMTQSPSSLSASVGDRVTITCWASQNIRSYLNWYQQTPGNAPKVLIYTASSFQSGVPSRFSDSGSGTEFTLTITTLQPEDFATYYCQQSSSPPYTFGQGTTLEIK

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	9

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6. Citations (1)

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resolution	2.930 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.93 Å
resolution_method	—
num_particles	201510

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

CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H33

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)