SAXSdb — 9x5y

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemagglutinin HA1 chain

Influenza B virus (B/Brisbane/60/2008)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 12 其他Polymer 12 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain A； UniProt 1–362 Chain B； UniProt 363–550 Chain E； UniProt 1–362 Chain F； UniProt 363–550 Chain G； UniProt 1–362 Chain I； UniProt 363–550	Not recorded	BO-6B heavy chain × 3 BO-6B light chain × 3 ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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 ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.65 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9X5Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FQK Influenza B/Brisbane/60/2008 hemagglutinin Fab CR8059 complex Deposited 2012-06-25	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 16–362（347 aa） Fragment：UNP residues 16-362 Chain B 363–538（176 aa） Fragment：UNP residues 363-538	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 5.65 Å R-free 0.324
4FQK Influenza B/Brisbane/60/2008 hemagglutinin Fab CR8059 complex Deposited 2012-06-25	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain C 16–362（347 aa） Fragment：UNP residues 16-362 Chain D 363–538（176 aa） Fragment：UNP residues 363-538	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 5.65 Å R-free 0.324
4FQM Structure of B/Brisbane/60/2008 Influenza Hemagglutinin Deposited 2012-06-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 16–362（347 aa） Fragment：UNP residues 16-362 Chain B 363–538（176 aa） Fragment：UNP residues 363-538 Chain C 16–362（347 aa） Fragment：UNP residues 16-362 Chain D 363–538（176 aa） Fragment：UNP residues 363-538 Chain E 16–362（347 aa） Fragment：UNP residues 16-362 Chain F 363–538（176 aa） Fragment：UNP residues 363-538	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；295 K；20% PEG3350, 160 mM sodium fluoride, 20 mM Tris, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.45 Å R-free 0.268
4FQM Structure of B/Brisbane/60/2008 Influenza Hemagglutinin Deposited 2012-06-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric	Chain G 16–362（347 aa） Fragment：UNP residues 16-362 Chain H 363–538（176 aa） Fragment：UNP residues 363-538 Chain I 16–362（347 aa） Fragment：UNP residues 16-362 Chain J 363–538（176 aa） Fragment：UNP residues 363-538 Chain K 16–362（347 aa） Fragment：UNP residues 16-362 Chain L 363–538（176 aa） Fragment：UNP residues 363-538	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；295 K；20% PEG3350, 160 mM sodium fluoride, 20 mM Tris, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.45 Å R-free 0.268
9X5W B/Brisbane/60/2008 HA in complex with BP-1A Deposited 2025-10-14	Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–362（362 aa） Chain B 363–550（188 aa） Chain C 1–362（362 aa） Chain D 363–550（188 aa） Chain E 1–362（362 aa） Chain F 363–550（188 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å
9X5X B/Brisbane/60/2008 HA in complex with FV2DP1-1B Deposited 2025-10-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–362（362 aa） Chain B 363–550（188 aa） Chain C 1–362（362 aa） Chain D 363–550（188 aa） Chain E 1–362（362 aa） Chain F 363–550（188 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.76 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C0LT38_9INFB
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–362； UniProt 1–362 Author chain E； PDBConstruct 1–362； UniProt 1–362 Author chain G； PDBConstruct 1–362； UniProt 1–362 Author chain B； PDBConstruct 1–188； UniProt 363–550 Author chain F； PDBConstruct 1–188； UniProt 363–550 Author chain I； PDBConstruct 1–188； UniProt 363–550

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9x5y
Deposition date deposition_date	2025-10-14
Structure title title	B/Brisbane/60/2008 HA in complex with BO-6B
Keywords keywords	Hemagglutinin, HA, antibody, influenza B virus, BO-6B, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	44.88 Å
Radius of gyration Rg (electron density) rg_electron	44.64 Å
Forward intensity I(0) i0	774094000.00
Molecular weight molecular_weight	225860.0 kDa
Excluded volume excluded_volume	281380 Å³
Envelope volume envelope_volume	384050 Å³
Hydration-shell volume shell_volume	71362 Å³
Envelope diameter envelope_diameter	141.3 Å
Shell Rg shell_rg	48.36 Å
Envelope Rg envelope_rg	45.35 Å
Shape Rg shape_rg	44.64 Å
Total Rg total_rg	44.80 Å
Total atoms total_atoms	15870
Residues n_residues	1995
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	141.3 Å
Rg (real space) rg_real	44.71 Å
Rg uncertainty (real space) rg_real_error	1.36 Å
I(0) (real space) i0_real	7.7410e+08
I(0) uncertainty (real space) i0_real_error	1.5070e+07
Rg (reciprocal space) rg_reciprocal	44.88 Å
I(0) (reciprocal space) i0_reciprocal	774200000.0000
Solution quality estimate total_estimate	0.9013
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	56.5 Å
Skewness Skewness skewness	0.119
Kurtosis Kurtosis kurtosis	-0.690
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	124600000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.859

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin HA1 chain
Molecular weight formula_weight	39285.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,A,E
Atom count atom_count	15930

MKAIIVLLMVVTSNADRICTGITSSNSPHVVKTATQGEVNVTGVIPLTTTPTKSHFANLKGTETRGKLCPKCLNCTDLDVALGRPKCTGKIPSARVSILHEVRPVTSGCFPIMHDRTKIRQLPNLLRGYEHIRLSTHNVINAENAPGGPYKIGTSGSCPNITNGNGFFATMAWAVPKNDKNKTATNPLTIEVPYICTEGEDQITVWGFHSDNETQMAKLYGDSKPQKFTSSANGVTTHYVSQIGGFPNQTEDGGLPQSGRIVVDYMVQKSGKTGTITYQRGILLPQKVWCASGRSKVIKGSLPLIGEADCLHEKYGGLNKSKPYYTGEHAKAIGNCPIWVKTPLKLANGTKYRPPAKLLKER

来源 Source

来源生物 organism	Influenza B virus (B/Brisbane/60/2008)
NCBI Class编号 ncbi_taxonomy_id	604436
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Hemagglutinin HA2 chain
Molecular weight formula_weight	25562.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,B,F

GFFGAIAGFLEGGWEGMIAGWHGYTSHGAHGVAVAADLKSTQEAINKITKNLNSLSELEVKNLQRLSGAMDELHNEILELDEKVDDLRADTISSQIELAVLLSNEGIINSEDEHLLALERKLKKMLGPSAVEIGNGCFETKHKCNQTCLDRIAAGTFDAGEFSLPTFDSLNITAASLNDDGLDNHTILDIRSLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH

来源 Source

来源生物 organism	Influenza B virus (B/Brisbane/60/2008)
NCBI Class编号 ncbi_taxonomy_id	604436
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	BO-6B heavy chain
Molecular weight formula_weight	50954.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,C,H

MGWSCIILFLVATATGVHSEVQLVESGGVVVQPGGSLRLSCAASGLNFSNFAMHWVRQAPGKGLEWVSVISWDGGTTFYADSVEGRFTISRDNNKNSLYLEMSSLRPEDTALYYCAQASSWGFFDSWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 4 Entity 4 polymer

Description description	BO-6B light chain
Molecular weight formula_weight	25544.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,D,L

MGWSCIILFLVATATGVHSEIVLTQSPGTLSLSPGQRATLSCRASQRVDSNYLGWYQQKPGQAPRLLIYGASNRATGIPDRFGGSGSGTDFTLTISRLEPEDIAVYSCQHFGDSWWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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 ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	man
Copy count entity_count	3

Entity 6 Entity 6 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	9

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	9

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.65 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	330198

fit	/app/data/saxs_computation/x5/9x5y/9x5y.fit
pddf	/app/data/pr_computation/x5/9x5y/9x5y.pr.out
profile	/app/data/saxs_computation/x5/9x5y/9x5y.dat

B/Brisbane/60/2008 HA in complex with BO-6B

1. Protein Identity and Related Structures Protein Identity & Related Structures

Hemagglutinin HA1 chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)