SAXSdb — 9yts

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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 × 10 其他Polymer 2 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 135–572 Chain F； UniProt 135–572	Not recorded	PIV3HN-09 Fab HC × 2 PIV3HN-09 Fab KC × 2 5217-2 Fab HC × 2 5217-2 Fab KC × 2 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	ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions	Resolution 3.29 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 9YTS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9B2W PIV3 HN with Fab 13 Deposited 2024-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 125–572（448 aa） Chain D 125–572（448 aa）	Not recorded	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
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 construct Different oligomeric state 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 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
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 construct	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_PI3H4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–438； UniProt 135–572 Author chain F； PDBConstruct 1–438； UniProt 135–572

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yts
Deposition date deposition_date	2025-10-21
Structure title title	Cryo-EM structure of the parainfluenza virus hemagglutinin-neuraminidase protein in complex with the human antibodies 5217-2 and PIV3HN-09
Keywords keywords	antibody, viral protein, complex, 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	43.61 Å
Radius of gyration Rg (electron density) rg_electron	43.47 Å
Forward intensity I(0) i0	582487000.00
Molecular weight molecular_weight	196330.0 kDa
Excluded volume excluded_volume	244980 Å³
Envelope volume envelope_volume	334390 Å³
Hydration-shell volume shell_volume	65632 Å³
Envelope diameter envelope_diameter	158.2 Å
Shell Rg shell_rg	46.74 Å
Envelope Rg envelope_rg	43.50 Å
Shape Rg shape_rg	43.47 Å
Total Rg total_rg	43.62 Å
Total atoms total_atoms	13811
Residues n_residues	1784
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	146.7 Å
Rg (real space) rg_real	43.69 Å
Rg uncertainty (real space) rg_real_error	1.64 Å
I(0) (real space) i0_real	5.8250e+08
I(0) uncertainty (real space) i0_real_error	1.1320e+07
Rg (reciprocal space) rg_reciprocal	43.61 Å
I(0) (reciprocal space) i0_reciprocal	582400000.0000
Solution quality estimate total_estimate	0.8610
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.0 Å
Skewness Skewness skewness	0.435
Kurtosis Kurtosis kurtosis	0.010
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	69760000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.650

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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-neuraminidase
Molecular weight formula_weight	48941.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,F
Atom count atom_count	13811

QEVLPQRITHDVGIKPLNPDDFWRCTSGLPSLMKTPKIRLMPGPGLLAMPTTVDGCVRTPSLVINDLIYAYTSNLITRGCQDIGKSYQVLQIGIITVNSDLVPDLNPRISHTFNINDNRKSCSLALLNTDVYQLCSTPKVDERSDYASSGIEDIVLDIVNYDGSISTTRFKNNNISFDQPYAALYPSVGPGIYYKGKIIFLGYGGLEHPINENVICNTTGCPGKTQRDCNQASHSPWFSDRRMVNSIIVADKGLNSIPKLKVWTISMRQNYWGSEGRLLLLGNKIYIYTRSTSWHSKLQLGIIDITDYSDIRIKWTWHNVLSRPGNNECPWGHSCPDGCITGVYTDAYPLNPTGSIVSSVILDSQKSRVNPVITYSTATERVNELAILNRTLSAGYTTTSCITHYNKGYCFHIVEINHKSLNTFQPMLFKTEIPKSCS

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	PIV3HN-09 Fab HC
Molecular weight formula_weight	13375.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QVQLQESGPGLVKPSETLSLTCTVSGGSVSSGSYYWSWIRQPPGKGLEWIGDIFTSGSTSYSPSLKSRVTISLDGSKNHFSLKLRSVSSADAAVYYCARESWEGAYLKYFDYWGQGTLVTVSS

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	PIV3HN-09 Fab KC
Molecular weight formula_weight	11727.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EIVLTQSPATLSLSPGERATLSCRASQSVSTYLAWYQQKPGQAPRLLMYDASNRATGIPARFSGSGSGTDFTLTISSLESEDFAVYYCQQRSIRPWTFGQGTKVEIK

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 polymer

Description description	5217-2 Fab HC
Molecular weight formula_weight	12542.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EVHLLESGGGLVQPGGSRRISCAASGFSFGSYAMSWVRQAPGKGLEWVSTITSSGESTDYADSVKGRFIISRDNAKNTLDLLMNSLRAGDTAVYYCAKGGAVVLSAMDVWGQGTTVTVSS

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 5 Entity 5 polymer

Description description	5217-2 Fab KC
Molecular weight formula_weight	11559.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DIQLTQSPSSLSASVGDRVTITCQASHDISNYLNWYQQKPGKAPKLLIYDASNLETGVPPRFSGGGSGTHFSLTISSLQPEDIATYYCQQDDSLPLTFGPGTKVEIK

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 6 Entity 6 branched

Description description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	367.3 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

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

Resolution resolution	3.29 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	238

fit	/app/data/saxs_computation/yt/9yts/9yts.fit
pddf	/app/data/pr_computation/yt/9yts/9yts.pr.out
profile	/app/data/saxs_computation/yt/9yts/9yts.dat

Cryo-EM structure of the parainfluenza virus hemagglutinin-neuraminidase protein in complex with the human antibodies 5217-2 and PIV3HN-09

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

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 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)