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9y3y

Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 49_C09 antibody

Method: X-RAY DIFFRACTION D_max: 230.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y3y
deposition_date	2025-09-02
title	Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 49_C09 antibody
keywords	Hemagglutinin, Head antibody, Influenza, Complex, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
method	X-RAY DIFFRACTION

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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	76.33 Å
rg_electron	77.44 Å
i0	610768000.00
molecular_weight	205160.0 kDa
excluded_volume	255370 Å³
envelope_volume	461490 Å³
shell_volume	56350 Å³
envelope_diameter	290.2 Å
shell_rg	65.57 Å
envelope_rg	74.62 Å
shape_rg	77.43 Å
total_rg	77.24 Å
total_atoms	14445
n_residues	1812
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	230.8 Å
rg_real	74.44 Å
rg_real_error	1.70 Å
i0_real	6.0320e+08
i0_real_error	1.3510e+07
rg_reciprocal	72.83 Å
i0_reciprocal	605300000.0000
total_estimate	0.8090
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	92.3 Å
skewness	0.405
kurtosis	-0.468
angular_range	— – 0.1000 Å⁻¹
current_alpha	0.0474
highest_alpha	12180000.0000
n_real_points	21
gnom_version	4.1.3
quality_criteria	AN1: 0.001; Oscil: 0.746; Stabil: 0.983; Sysdev: 1.000; Positv: 1.000; Valcen: 0.853; Smooth: 0.386

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Hemagglutinin
formula_weight	36243.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,A
atom_count	14461

ADPGDTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPSTSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPS

Source

organism	Influenza A virus (A/California/04/2009(H1N1))
ncbi_taxonomy_id	641501
host_organism	Trichoplusia ni

Entity 2 polymer

description	Hemagglutinin
formula_weight	20206.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,B

GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDSGR

Source

organism	Influenza A virus (A/California/04/2009(H1N1))
ncbi_taxonomy_id	641501
host_organism	Trichoplusia ni

Entity 3 polymer

description	Antibody 49_C09 light chain
formula_weight	22939.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,F

SYVLTQPPSVSVAPGQTARIPCGGNNIGMKTVHWYQQRPGQAPVVVVYDDSRRPSGIPERFSGSNSGNTATLTISRVEAGDEADYYCQVWDSSVNHWVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	Antibody 49_C09 heavy chain
formula_weight	24094.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,E

QSTLKESGPTLVKPTETLTLTCTFSGFSLHTSGVGVGWIRQPPGKALECLALIYWNDDARYSPSLQSRLTITKDTSKNQVVLTMSNMDPVDTATYYCAHKGGGRDGYNSAAFDVWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	syn
entity_count	2

Entity 6 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

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6. Citations (1)

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length_a	166.919 Å
length_b	166.919 Å
length_c	347.947 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 3 2 1
int_tables_number	150
crystal_system	—

resolution	3.800 Å
resolution_low	49.710 Å
r_factor	0.2067
r_work	0.2051
r_free	0.2400

fit	/app/data/saxs_computation/y3/9y3y/9y3y.fit
pddf	/app/data/pr_computation/y3/9y3y/9y3y.pr.out
profile	/app/data/saxs_computation/y3/9y3y/9y3y.dat

Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 49_C09 antibody

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

Diffraction

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 branched

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)