← Back to search

9y3x

Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 3_H2 antibody

Method: X-RAY DIFFRACTION D_max: 180.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9y3x
deposition_date	2025-09-02
title	Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 3_H2 antibody
keywords	Hemagglutinin, Head antibody, Influenza, Complex, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	49.51 Å
rg_electron	51.16 Å
i0	163751000.00
molecular_weight	103300.0 kDa
excluded_volume	128720 Å³
envelope_volume	185750 Å³
shell_volume	36322 Å³
envelope_diameter	188.6 Å
shell_rg	42.73 Å
envelope_rg	51.65 Å
shape_rg	51.15 Å
total_rg	50.82 Å
total_atoms	7271
n_residues	911
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

▼

3. P(r) Analysis (GNOM)

dmax	180.2 Å
rg_real	51.20 Å
rg_real_error	2.85 Å
i0_real	1.6380e+08
i0_real_error	3.7040e+06
rg_reciprocal	49.53 Å
i0_reciprocal	163400000.0000
total_estimate	0.6253
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	28.1 Å
skewness	0.723
kurtosis	-0.240
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	6575000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.273; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.096; Smooth: 0.211

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Hemagglutinin
formula_weight	36243.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E
atom_count	7271

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	1

Polymer

type	polypeptide(L)
strand_id	F

GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDGITNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDSGR

Source

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

Entity 3 polymer

description	Antibody 3_H2 heavy chain
formula_weight	24185.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QGTLKESGPAMVKPTQTLTLTCTFSGFSLDTSGMCVAWIRQPPGKALEWLALFDWDNNKYYSPSLKTRLNMSKGRSRNQVVLTMTNMDPVDTGTYYCARKVYGSFYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	Antibody 3_H2 light chain
formula_weight	23573.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIVLTQSPATLSLSPGDSATLSCRASQDVSANLAWYQQKPGQAPRLVIYDATNRATGIPARFSGSGLGTDFTLTISSLEPEDFAVYYCQQRSNWPPVYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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	man
entity_count	1

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	1

▶

6. Citations (1)

▶

length_a	130.894 Å
length_b	130.894 Å
length_c	142.840 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 3 2 1
int_tables_number	150
crystal_system	—

resolution	3.390 Å
resolution_low	48.250 Å
r_factor	0.2099
r_work	0.2043
r_free	0.2608

fit	/app/data/saxs_computation/y3/9y3x/9y3x.fit
pddf	/app/data/pr_computation/y3/9y3x/9y3x.pr.out
profile	/app/data/saxs_computation/y3/9y3x/9y3x.dat

Crystal structure of hemagglutinin from H1N1 Influenza A virus A/California/04/2009 bound to the 3_H2 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 (6)

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)