SAXSdb — 9dzq

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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	Protein heterocomplex Heteromer Protein × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 125–572 Chain B； UniProt 125–572	Not recorded	Human antibody PIV3HN-05 heavy chain × 2 Human antibody PIV3HN-05 light chain × 2 Human antibody PIV3HN-13 heavy chain × 2 Human antibody PIV3HN-13 light chain × 2	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

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 9DZQ	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 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
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 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 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 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 B； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9dzq
Deposition date deposition_date	2024-10-16
Structure title title	CryoEM structure of the human antibodies PIV3HN-05 and PIV3HN-13 in complex with the parainfluenza virus hemagglutinin-neuraminidase protein
Keywords keywords	Hemagglutinin-neuraminidase, human monoclonal antibody, 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	36.42 Å
Radius of gyration Rg (electron density) rg_electron	35.53 Å
Forward intensity I(0) i0	336203000.00
Molecular weight molecular_weight	147490.0 kDa
Excluded volume excluded_volume	183610 Å³
Envelope volume envelope_volume	242660 Å³
Hydration-shell volume shell_volume	55562 Å³
Envelope diameter envelope_diameter	124.6 Å
Shell Rg shell_rg	42.75 Å
Envelope Rg envelope_rg	36.24 Å
Shape Rg shape_rg	35.56 Å
Total Rg total_rg	35.90 Å
Total atoms total_atoms	10434
Residues n_residues	1487
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	114.7 Å
Rg (real space) rg_real	36.24 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	3.3620e+08
I(0) uncertainty (real space) i0_real_error	5.1660e+06
Rg (reciprocal space) rg_reciprocal	36.35 Å
I(0) (reciprocal space) i0_reciprocal	336200000.0000
Solution quality estimate total_estimate	0.9018
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	50.7 Å
Skewness Skewness skewness	0.124
Kurtosis Kurtosis kurtosis	-0.542
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	90010000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.939

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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	A,B
Atom count atom_count	10434

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	Human antibody PIV3HN-05 heavy chain
Molecular weight formula_weight	24696.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EVQLVESGGGVVQPGGSLRLSCVASGLSLSPNWMHWVRQAPGKGLVWVSRISDNGDTTNYAGSVMGRFTISRDNAKNTLYLQMNNLRADDTAVYFCVRESAVISSPSWGLYDTAYHFDPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

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	Human antibody PIV3HN-05 light chain
Molecular weight formula_weight	22877.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QSVLTQPPSASGTPGQGVTISCSGSNSNIGTNAVDWYQQFPGTAPRLLIFNDNQRPSGVPDRFSGSRSGTSASLAISGLQSEDEAVYYCATWDDSLNGPVVFGGGTKLTVLRQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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	Human antibody PIV3HN-13 heavy chain
Molecular weight formula_weight	23686.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EVQLLESGGALVQPGGSLRVSCAASGFSFSSYAMSWLRQTPGKGLEWVSAIGGSGHSTYYADSVQGRFTVSRDNSKDTLYLQMNSLRAEDTAVYYCAKFFRSDGVFHFDYWGPGNPGSPSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

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	Human antibody PIV3HN-13 light chain
Molecular weight formula_weight	23785.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DIVMTQSPLSLPVTPGEPASISCRSSQSLRHSDGNNYLDWYLQKPGQSPQLLIYLGSNRASGVPDRFSGSGSGSDFTLKISRVEAEDVGVYYCMQALQTPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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

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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	triclinic

Resolution resolution	3.57 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	139192

fit	/app/data/saxs_computation/dz/9dzq/9dzq.fit
pddf	/app/data/pr_computation/dz/9dzq/9dzq.pr.out
profile	/app/data/saxs_computation/dz/9dzq/9dzq.dat

CryoEM structure of the human antibodies PIV3HN-05 and PIV3HN-13 in complex with the parainfluenza virus hemagglutinin-neuraminidase protein

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)