9b2w

PIV3 HN with Fab 13

Method: X-RAY DIFFRACTION D_max: 166.8 Å Quality: GOOD

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

Hemagglutinin-neuraminidase

Human respirovirus 3

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 × 6 其他Polymer 5 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 125–572 Chain D； UniProt 125–572	Not recorded	Fab 13 Heavy Chain × 2 Fab 13 Light Chain × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；300 K；0.1M Ammonium sulfate, 0.1M MES pH 6.5, 15% (w/v) PEG 4000	Resolution 2.51 Å R-free 0.264

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 9B2W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9DZQ CryoEM structure of the human antibodies PIV3HN-05 and PIV3HN-13 in complex with the parainfluenza virus hemagglutinin-neuraminidase protein Deposited 2024-10-16	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 125–572（448 aa） Chain B 125–572（448 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Tris, pH 7.5 120 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
9YQ6 Cryo-EM structure of the parainfluenza virus hemagglutinin-neuraminidase protein in complex with the human antibodies PIV3HN-09 and PIV3HN-13 Deposited 2025-10-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain A 135–572（438 aa） Chain F 135–572（438 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.95 Å
9YTS Cryo-EM structure of the parainfluenza virus hemagglutinin-neuraminidase protein in complex with the human antibodies 5217-2 and PIV3HN-09 Deposited 2025-10-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain A 135–572（438 aa） Chain F 135–572（438 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.29 Å
9ZB5 Cryo-EM structure of the parainfluenza virus hemagglutinin-neuraminidase protein in complex with the human antibodies PIV3HN-05 and PIV3HN-13 Deposited 2025-11-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric	Chain F 125–572（448 aa） Chain J 125–572（448 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.29 Å

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

View Construct and Data Evidence

UniProt name	Q81080_9MONO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–461； UniProt 125–572 Author chain D； PDBConstruct 14–461； UniProt 125–572

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9b2w
Deposition date deposition_date	2024-03-17
Structure title title	PIV3 HN with Fab 13
Keywords keywords	HN, hemagglutinin neuraminidase, complex, antibody complex, VIRAL PROTEIN, VIRAL PROTEIN-Immune System complex; VIRAL PROTEIN/Immune System
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	45.36 Å
Radius of gyration Rg (electron density) rg_electron	45.59 Å
Forward intensity I(0) i0	567497000.00
Molecular weight molecular_weight	193010.0 kDa
Excluded volume excluded_volume	240440 Å³
Envelope volume envelope_volume	321320 Å³
Hydration-shell volume shell_volume	61923 Å³
Envelope diameter envelope_diameter	178.0 Å
Shell Rg shell_rg	46.11 Å
Envelope Rg envelope_rg	46.59 Å
Shape Rg shape_rg	45.57 Å
Total Rg total_rg	45.68 Å
Total atoms total_atoms	13565
Residues n_residues	1731
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	166.8 Å
Rg (real space) rg_real	45.72 Å
Rg uncertainty (real space) rg_real_error	2.05 Å
I(0) (real space) i0_real	5.6750e+08
I(0) uncertainty (real space) i0_real_error	1.0680e+07
Rg (reciprocal space) rg_reciprocal	45.36 Å
I(0) (reciprocal space) i0_reciprocal	567300000.0000
Solution quality estimate total_estimate	0.8155
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.6 Å
Skewness Skewness skewness	0.554
Kurtosis Kurtosis kurtosis	0.005
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	66480000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.735; Smooth: 0.779

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin-neuraminidase
Molecular weight formula_weight	51625.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,A
Atom count atom_count	13578

HHHHHHSLVPRGSISEITIRNDNQEVLPQRITHDVGIKPLNPDDFWRCTSGLPSLMKTPKIRLMPGPGLLAMPTTVDGCVRTPSLVINDLIYAYTSNLITRGCQDIGKSYQVLQIGIITVNSDLVPDLNPRISHTFNINDNRKSCSLALLNTDVYQLCSTPKVDERSDYASSGIEDIVLDIVNYDGSISTTRFKNNNISFDQPYAALYPSVGPGIYYKGKIIFLGYGGLEHPINENVICNTTGCPGKTQRDCNQASHSPWFSDRRMVNSIIVADKGLNSIPKLKVWTISMRQNYWGSEGRLLLLGNKIYIYTRSTSWHSKLQLGIIDITDYSDIRIKWTWHNVLSRPGNNECPWGHSCPDGCITGVYTDAYPLNPTGSIVSSVILDSQKSRVNPVITYSTATERVNELAILNRTLSAGYTTTSCITHYNKGYCFHIVEINHKSLNTFQPMLFKTEIPKSCS

来源 Source

来源生物 organism	Human respirovirus 3
NCBI Class编号 ncbi_taxonomy_id	11216
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Fab 13 Heavy Chain
Molecular weight formula_weight	23468.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

EVQLLESGGALVQPGGSLRVSCAASGFSFSSYAMSWLRQTPGKGLEWVSAIGGSGHSTYYADSVQGRFTVSRDNSKDTLYLQMNSLRAEDTAVYYCAKFFRSDGVFHFDYWGPGNPGSPSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

来源 Source

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

Entity 3 Entity 3 polymer

Description description	Fab 13 Light Chain
Molecular weight formula_weight	23900.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

DDIVMTQSPLSLPVTPGEPASISCRSSQSLRHSDGNNYLDWYLQKPGQSPQLLIYLGSNRASGVPDRFSGSGSGSDFTLKISRVEAEDVGVYYCMQALQTPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

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

Entity 4 Entity 4 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	1

Entity 5 Entity 5 branched

Description description	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	586.5 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 branched

Description description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 9 Entity 9 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	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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8. Citations (1)

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Unit-cell length a length_a	81.273 Å
Unit-cell length b length_b	129.353 Å
Unit-cell length c length_c	89.454 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	34.760 Å
R factor r_factor	0.2214
R_work r_work	0.2192
R_free r_free	0.2644

fit	/app/data/saxs_computation/b2/9b2w/9b2w.fit
pddf	/app/data/pr_computation/b2/9b2w/9b2w.pr.out
profile	/app/data/saxs_computation/b2/9b2w/9b2w.dat

PIV3 HN with Fab 13

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

Hemagglutinin-neuraminidase

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (10)

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 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)