SAXSdb — 9cjz

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

Hemagglutinin HA1 chain

Influenza A virus

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 × 12 PDB declaration: 12-meric（12） Consistent with protein copy count	Chain A； UniProt 18–343 Chain B； UniProt 344–519 Chain C； UniProt 18–343 Chain D； UniProt 344–519 Chain E； UniProt 18–343 Chain F； UniProt 344–519	Not recorded	3-E04 Heavy chain × 3 3-E04 Light chain × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.80 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 9CJZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5C0R Crystal Structure of a Generation 3 Influenza Hemagglutinin Stabilized Stem Complexed with the Broadly Neutralizing Antibody C179 Deposited 2015-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 18–49（32 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485 Chain A 328–402（75 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485 Chain A 436–517（82 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；15% (w/v) PEG 1500, 5% (v/v) MPD, 200 mM ammonium chloride, 100 mM Tris, pH 8.5	Resolution 3.19 Å R-free 0.251
5C0S Crystal structure of a generation 4 influenza hemagglutinin stabilized stem in complex with the broadly neutralizing antibody CR6261 Deposited 2015-06-12	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 18–49（32 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485 Chain A 328–402（75 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485 Chain A 436–517（82 aa） Fragment：UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；7% (w/v) PEG 4000, 4.5% (v/v) isopropanol, 100 mM imidazole, pH 6.5	Resolution 4.30 Å R-free 0.310
7MFG Cryo-EM structure of the VRC310 clinical trial, vaccine-elicited, human antibody 310-030-1D06 Fab in complex with an H1 NC99 HA trimer Deposited 2021-04-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 18–343（326 aa） Chain C 18–343（326 aa） Chain G 18–343（326 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.87 Å
8D21 Cryo-EM structure of the VRC321 clinical trial, vaccine-elicited, human antibody 1B06 in complex with a stabilized NC99 HA trimer Deposited 2022-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 18–343（326 aa） Chain D 18–343（326 aa） Chain I 18–343（326 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；PBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
8TP3 H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1F05 Deposited 2023-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–343（343 aa） Chain B 344–565（222 aa） Chain C 1–343（343 aa） Chain D 344–565（222 aa） Chain G 1–343（343 aa） Chain I 344–565（222 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8TP5 H1 hemagglutinin (NC99) in complex with RBS-targeting Fab 1-1-1E04 Deposited 2023-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 18–339（322 aa） Chain B 344–514（171 aa） Chain C 18–339（322 aa） Chain D 344–514（171 aa） Chain G 18–339（322 aa） Chain I 344–514（171 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8TPA H1 hemagglutinin (NC99) in complex with medial-junction-targeting Fab 2-2-1G06 Deposited 2023-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1–343（343 aa） Chain B 344–565（222 aa） Chain C 1–343（343 aa） Chain F 344–565（222 aa） Chain G 1–343（343 aa） Chain K 344–565（222 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9B2M Hemagglutinin H1 New Caledonia 1999 in complex with monoclonal antibody Fab 43_S0008 Deposited 2024-03-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain A 1–339（339 aa） Chain B 340–565（226 aa） Chain C 1–339（339 aa） Chain D 340–565（226 aa） Chain G 1–339（339 aa） Chain I 340–565（226 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；TBS cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9CJY CryoEM structure of NC99 hemagglutinin trimer in complex with Fab BB798E 3-C07 Deposited 2024-07-08	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 18–343（326 aa） Chain B 344–519（176 aa） Chain C 18–343（326 aa） Chain D 344–519（176 aa） Chain E 18–343（326 aa） Chain F 344–519（176 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q6WG00_9INFA
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–326； UniProt 18–343 Author chain C； PDBConstruct 1–326； UniProt 18–343 Author chain E； PDBConstruct 1–326； UniProt 18–343 Author chain B； PDBConstruct 1–176； UniProt 344–519 Author chain D； PDBConstruct 1–176； UniProt 344–519 Author chain F； PDBConstruct 1–176； UniProt 344–519

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	9cjz
Deposition date deposition_date	2024-07-08
最后修订 last_revision	2025-07-09
Structure title title	CryoEM structure of NC99 hemagglutinin trimer in complex with Fab T009 3-E04
Keywords keywords	Immune system, Hemagglutinin, Fab, Macaque, VIRAL PROTEIN; VIRAL PROTEIN
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	49.44 Å
Radius of gyration Rg (electron density) rg_electron	49.55 Å
Forward intensity I(0) i0	702968000.00
Molecular weight molecular_weight	218720.0 kDa
Excluded volume excluded_volume	272830 Å³
Envelope volume envelope_volume	404090 Å³
Hydration-shell volume shell_volume	69698 Å³
Envelope diameter envelope_diameter	157.6 Å
Shell Rg shell_rg	51.55 Å
Envelope Rg envelope_rg	48.55 Å
Shape Rg shape_rg	49.57 Å
Total Rg total_rg	49.55 Å
Total atoms total_atoms	15429
Residues n_residues	1909
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	157.8 Å
Rg (real space) rg_real	49.47 Å
Rg uncertainty (real space) rg_real_error	1.42 Å
I(0) (real space) i0_real	7.0300e+08
I(0) uncertainty (real space) i0_real_error	1.3180e+07
Rg (reciprocal space) rg_reciprocal	49.44 Å
I(0) (reciprocal space) i0_reciprocal	702900000.0000
Solution quality estimate total_estimate	0.8832
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.2 Å
Skewness Skewness skewness	0.241
Kurtosis Kurtosis kurtosis	-0.733
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	64660000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.670

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Hemagglutinin HA1 chain
Molecular weight formula_weight	36417.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	15429

DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCLLKGIAPLQLGNCSVAGWILGNPECELLISKESWSYIVETPNPENGTCYPGYFADYEELREQLSSVSSFERFEIFPKESSWPNHTVTGVSASCSHNGKSSFYRNLLWLTGKNGLYPNLSKSYVNNKEKEVLVLWGVHHPPNIGNQRALYHTENAYVSVVSSHYSRRFTPEIAKRPKVRDQEGRINYYWTLLEPGDTIIFEANGNLIAPWYAFALSRGFGSGIITSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTIGECPKYVRSAKLRMVTGLRNIPSIQSR

来源 Source

来源生物 organism	Influenza A virus
NCBI Class编号 ncbi_taxonomy_id	11320
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Hemagglutinin HA2 chain
Molecular weight formula_weight	25288.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

GLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINQITNKVNSVIEKMNTQFTAVGKEFNKLERRMENLNKKVDDGFLDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQLKNNAKEIGNGCFEFYHKCNNECMESVKNGTYDYPKYSEESKLNREKIDGVSGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH

来源 Source

来源生物 organism	Influenza A virus
NCBI Class编号 ncbi_taxonomy_id	11320
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	3-E04 Heavy chain
Molecular weight formula_weight	13082.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYGLSWVRQAPGKGLEWVSYISNSGISTYYADSVKGRFTISRDNSKNTVSLQLNSLTPEDTAVYYCAKKGSTLIPYTWFDVWGPGVLVTVSS

来源 Source

来源生物 organism	Macaca fascicularis
NCBI Class编号 ncbi_taxonomy_id	9541
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	3-E04 Light chain
Molecular weight formula_weight	11560.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

EIVMTQSPATLSLSPGERATLSCRASQSVSTSLAWYQQKPGQAPKLLIYGASSRATGIPDRFSGSGSGTEFTLTISSLEPEDVGVYYCQQDYNWPPLTFGGGTKVEIK

来源 Source

来源生物 organism	Macaca fascicularis
NCBI Class编号 ncbi_taxonomy_id	9541
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	—

Resolution resolution	3.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	160012

fit	/app/data/saxs_computation/cj/9cjz/9cjz.fit
pddf	/app/data/pr_computation/cj/9cjz/9cjz.pr.out
profile	/app/data/saxs_computation/cj/9cjz/9cjz.dat

CryoEM structure of NC99 hemagglutinin trimer in complex with Fab T009 3-E04

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)