SAXSdb — 9w20

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

Non-structural protein 1

dengue virus type 2

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 776–1127 Chain B； UniProt 776–1127 Chain a； UniProt 776–1127 Chain b； UniProt 776–1127	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.63 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 9W20	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9W1X DENV2 non-structural protein 1 (NS1) Loose Tetramer Conformation 2 Deposited 2025-07-26	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 776–1127（352 aa） Chain B 776–1127（352 aa） Chain a 776–1127（352 aa） Chain b 776–1127（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
9W1Y DENV2 non-structural protein 1 (NS1) with C-terminal mVenus Conformation 2 Deposited 2025-07-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 776–1127（352 aa） Chain B 776–1127（352 aa） Chain a 776–1127（352 aa） Chain b 776–1127（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å
9W1Z DENV2 non-structural protein 1 (NS1) Stable Tetramer Conformation 2 Deposited 2025-07-26	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 776–1127（352 aa） Chain B 776–1127（352 aa） Chain a 776–1127（352 aa） Chain b 776–1127（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
9W21 DENV2 non-structural protein 1 (NS1) Loose Tetramer Conformation 1 Deposited 2025-07-26	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 776–1127（352 aa） Chain B 776–1127（352 aa） Chain a 776–1127（352 aa） Chain b 776–1127（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
9W22 DENV2 non-structural protein 1 (NS1) Dimer Deposited 2025-07-26	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 776–1127（352 aa） Chain a 776–1127（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
9W23 DENV2 non-structural protein 1 (NS1) Stable Tetramer complexed with Heparin Deposited 2025-07-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 776–1127（352 aa） Chain B 776–1127（352 aa） Chain a 776–1127（352 aa） Chain b 776–1127（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
9W24 DENV2 non-structural protein 1 (NS1) with C-terminal mVenus fusion Deposited 2025-07-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 776–1127（352 aa） Chain B 776–1127（352 aa） Chain a 776–1127（352 aa） Chain b 776–1127（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9W25 DENV2 non-structural protein 1 (NS1) with C-terminal mVenus Conformation 1 Deposited 2025-07-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 776–1127（352 aa） Chain B 776–1127（352 aa） Chain a 776–1127（352 aa） Chain b 776–1127（352 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.30 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H9M645_9FLAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–352； UniProt 776–1127 Author chain B； PDBConstruct 1–352； UniProt 776–1127 Author chain a； PDBConstruct 1–352； UniProt 776–1127 Author chain b； PDBConstruct 1–352； UniProt 776–1127

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	9w20
Deposition date deposition_date	2025-07-26
Structure title title	DENV2 non-structural protein 1 (NS1) Stable Tetramer Conformation 1
Keywords keywords	Dengue virus; non-structural protein 1; NS1; flavivirus, 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	37.70 Å
Radius of gyration Rg (electron density) rg_electron	36.76 Å
Forward intensity I(0) i0	371035000.00
Molecular weight molecular_weight	153850.0 kDa
Excluded volume excluded_volume	191460 Å³
Envelope volume envelope_volume	267710 Å³
Hydration-shell volume shell_volume	58855 Å³
Envelope diameter envelope_diameter	116.6 Å
Shell Rg shell_rg	44.62 Å
Envelope Rg envelope_rg	36.30 Å
Shape Rg shape_rg	36.70 Å
Total Rg total_rg	37.44 Å
Total atoms total_atoms	10806
Residues n_residues	1354
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	115.8 Å
Rg (real space) rg_real	37.43 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	3.7100e+08
I(0) uncertainty (real space) i0_real_error	5.5670e+06
Rg (reciprocal space) rg_reciprocal	37.60 Å
I(0) (reciprocal space) i0_reciprocal	371100000.0000
Solution quality estimate total_estimate	0.8896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.4 Å
Skewness Skewness skewness	0.073
Kurtosis Kurtosis kurtosis	-0.459
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	78860000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.911

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (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	3.63 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	40652

Description description	Non-structural protein 1
Molecular weight formula_weight	40874.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,a,B,b
Atom count atom_count	10806

DENV2 non-structural protein 1 (NS1) Stable Tetramer Conformation 1

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

Non-structural protein 1

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	dengue virus type 2
NCBI Class编号 ncbi_taxonomy_id	11060
宿主生物 host_organism	Homo sapiens

fit	/app/data/saxs_computation/w2/9w20/9w20.fit
pddf	/app/data/pr_computation/w2/9w20/9w20.pr.out
profile	/app/data/saxs_computation/w2/9w20/9w20.dat