SAXSdb — 3ee9

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

Non-structural protein 1

Influenza A virus (A/Udorn/307/1972(H3N2))

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 84–205	Fragment：Effector domain (UNP residues 84-205)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：Batch；pH 5.5；298 K；20% (w/v) PEG400, 0.1M CH3COONa (pH5.5), 0.1M MgSO4, Batch, temperature 298K	Resolution 2.14 Å R-free 0.234
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 84–205	Fragment：Effector domain (UNP residues 84-205)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：Batch；pH 5.5；298 K；20% (w/v) PEG400, 0.1M CH3COONa (pH5.5), 0.1M MgSO4, Batch, temperature 298K	Resolution 2.14 Å R-free 0.234

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 3EE9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AIL N-TERMINAL FRAGMENT OF NS1 PROTEIN FROM INFLUENZA A VIRUS Deposited 1997-04-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–72（72 aa） Fragment：RNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；NATIVE CRYSTALS WERE GROWN FROM 50MM NAH2PO4, 100MM NACL, 1MM NAN3 AT PH 6.5; MERCURY DERIVATIVE CRYSTAL WAS PREPARED BY SOAKING THE NATIVE CRYSTAL IN 2MM CH3HGCL WITH 10% PEG 6000 AT PH 8.0; PLATINUM DERIVATIVE CRYSTAL WAS PREPARED BY SOAKING THE NATIVE CRYSTAL IN 4MM PT(NH3)2CL2 WITH 10% PEG 6000 AT PH 6.5.	Resolution 1.90 Å R-free 0.229
1NS1 RNA-BINDING DOMAIN OF NON-STRUCTURAL PROTEIN 1 FROM INFLUENZA VIRUS, NMR, 16 STRUCTURES Deposited 1997-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–73（73 aa） Fragment：RNA-BINDING DOMAIN, RESIDUES 1 - 73 Chain B 1–73（73 aa） Fragment：RNA-BINDING DOMAIN, RESIDUES 1 - 73	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；293 K	Resolution not provided
2RHK Crystal structure of influenza A NS1A protein in complex with F2F3 fragment of human cellular factor CPSF30, Northeast Structural Genomics Targets OR8C and HR6309A Deposited 2007-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 85–215（131 aa） Fragment：NS1A effector domain (UNP residues 85-215) Chain B 85–215（131 aa） Fragment：NS1A effector domain (UNP residues 85-215)	Not recorded	NO3 NITRATE ION × 5 ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293 K；0.5 M KNO3, 10% sucroes, 0.1M sodium acitate, pH 5.5, EVAPORATION, temperature 293K, pH 5.50	Resolution 1.95 Å R-free 0.234
2RHK Crystal structure of influenza A NS1A protein in complex with F2F3 fragment of human cellular factor CPSF30, Northeast Structural Genomics Targets OR8C and HR6309A Deposited 2007-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 85–215（131 aa） Fragment：NS1A effector domain (UNP residues 85-215) Chain B 85–215（131 aa） Fragment：NS1A effector domain (UNP residues 85-215)	Not recorded	NO3 NITRATE ION × 9 ZN ZINC ION × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293 K；0.5 M KNO3, 10% sucroes, 0.1M sodium acitate, pH 5.5, EVAPORATION, temperature 293K, pH 5.50	Resolution 1.95 Å R-free 0.234
2RHK Crystal structure of influenza A NS1A protein in complex with F2F3 fragment of human cellular factor CPSF30, Northeast Structural Genomics Targets OR8C and HR6309A Deposited 2007-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 85–215（131 aa） Fragment：NS1A effector domain (UNP residues 85-215)	Not recorded	NO3 NITRATE ION × 5 ZN ZINC ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293 K；0.5 M KNO3, 10% sucroes, 0.1M sodium acitate, pH 5.5, EVAPORATION, temperature 293K, pH 5.50	Resolution 1.95 Å R-free 0.234
2RHK Crystal structure of influenza A NS1A protein in complex with F2F3 fragment of human cellular factor CPSF30, Northeast Structural Genomics Targets OR8C and HR6309A Deposited 2007-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 85–215（131 aa） Fragment：NS1A effector domain (UNP residues 85-215) Chain B 85–215（131 aa） Fragment：NS1A effector domain (UNP residues 85-215)	Not recorded	NO3 NITRATE ION × 4 ZN ZINC ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；293 K；0.5 M KNO3, 10% sucroes, 0.1M sodium acitate, pH 5.5, EVAPORATION, temperature 293K, pH 5.50	Resolution 1.95 Å R-free 0.234
3EE8 Structure of NS1 effector domain Deposited 2008-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 84–205（122 aa） Fragment：Effector domain (UNP residues 84-205)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；12% (w/v) PEG3350, and 4% (v/v) Tacsimate (pH6.0), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.284
3EE8 Structure of NS1 effector domain Deposited 2008-09-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 84–205（122 aa） Fragment：Effector domain (UNP residues 84-205)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；12% (w/v) PEG3350, and 4% (v/v) Tacsimate (pH6.0), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.284
3KWG X-ray structure of NS1 effector domain W187A mutant Deposited 2009-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–205（128 aa） Fragment：NS1 effector domain	Mutation：W187A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；277 K；0.3M magnesium formate, 0.1M Bis-Tris , pH 5.5, EVAPORATION, temperature 277K	Resolution 2.21 Å R-free 0.233
3KWG X-ray structure of NS1 effector domain W187A mutant Deposited 2009-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 78–205（128 aa） Fragment：NS1 effector domain	Mutation：W187A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；277 K；0.3M magnesium formate, 0.1M Bis-Tris , pH 5.5, EVAPORATION, temperature 277K	Resolution 2.21 Å R-free 0.233
3KWG X-ray structure of NS1 effector domain W187A mutant Deposited 2009-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 78–205（128 aa） Fragment：NS1 effector domain Chain B 78–205（128 aa） Fragment：NS1 effector domain	Mutation：W187A Mutation：W187A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；277 K；0.3M magnesium formate, 0.1M Bis-Tris , pH 5.5, EVAPORATION, temperature 277K	Resolution 2.21 Å R-free 0.233
3KWI X-ray structure of NS1 effector domain W187Y mutant Deposited 2009-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–205（128 aa） Fragment：NS1 effector domain	Mutation：W187Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；277 K；0.3M magnesium formate and 0.1M Bis-Tris , pH 5.5, EVAPORATION, temperature 277K	Resolution 2.21 Å R-free 0.258
3KWI X-ray structure of NS1 effector domain W187Y mutant Deposited 2009-12-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 78–205（128 aa） Fragment：NS1 effector domain	Mutation：W187Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 5.5；277 K；0.3M magnesium formate and 0.1M Bis-Tris , pH 5.5, EVAPORATION, temperature 277K	Resolution 2.21 Å R-free 0.258

6 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NS1_I72A2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 84–205 Author chain B； PDBConstruct 1–122； UniProt 84–205

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	3ee9
Deposition date deposition_date	2008-09-04
Structure title title	Structure of NS1 effector domain
Keywords keywords	;Zinc finger receptor, Alternative splicing, Cytoplasm, Host-virus interaction, Interferon antiviral system evasion, Nucleus, RNA-binding, Suppressor of RNA silencing, VIRAL PROTEIN ;; VIRAL PROTEIN
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	20.43 Å
Radius of gyration Rg (electron density) rg_electron	19.82 Å
Forward intensity I(0) i0	12779300.00
Molecular weight molecular_weight	27360.0 kDa
Excluded volume excluded_volume	34576 Å³
Envelope volume envelope_volume	40259 Å³
Hydration-shell volume shell_volume	17575 Å³
Envelope diameter envelope_diameter	68.1 Å
Shell Rg shell_rg	25.46 Å
Envelope Rg envelope_rg	19.99 Å
Shape Rg shape_rg	19.84 Å
Total Rg total_rg	20.61 Å
Total atoms total_atoms	1919
Residues n_residues	240
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	68.5 Å
Rg (real space) rg_real	20.43 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.2780e+07
I(0) uncertainty (real space) i0_real_error	1.6760e+05
Rg (reciprocal space) rg_reciprocal	20.43 Å
I(0) (reciprocal space) i0_reciprocal	12780000.0000
Solution quality estimate total_estimate	0.8788
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.364
Kurtosis Kurtosis kurtosis	-0.339
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2300000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.821; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.969

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Non-structural protein 1
Molecular weight formula_weight	13796.0 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	2062

TPASRYITDMTIEELSRDWFMLMPKQKVEGPLCIRIDQAIMDKNIMLKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSFPGHTIEDVKNAIGVLIGGLEWNDNTVRVSKTLQRFAWGS

来源 Source

来源生物 organism	Influenza A virus (A/Udorn/307/1972(H3N2))
NCBI Class编号 ncbi_taxonomy_id	381517
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	136

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ee9a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.299 — Ns1 effector domain-like
Superfamily Superfamily superfamily	d.299.1 — Ns1 effector domain-like
Family Family family	d.299.1.1 — Ns1 effector domain-like

Domain ID domain_id	d3ee9b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.299 — Ns1 effector domain-like
Superfamily Superfamily superfamily	d.299.1 — Ns1 effector domain-like
Family Family family	d.299.1.1 — Ns1 effector domain-like

CATH v4.4 (2 domains)

Domain ID domain_id	3ee9A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	330 — Influenza virus non-structural protein, effector domain

Domain ID domain_id	3ee9B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	330 — Influenza virus non-structural protein, effector domain

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8. Citations (1)

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Unit-cell length a length_a	47.924 Å
Unit-cell length b length_b	61.456 Å
Unit-cell length c length_c	132.130 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1990
R_work r_work	0.1980
R_free r_free	0.2340

fit	/app/data/saxs_computation/ee/3ee9/3ee9.fit
pddf	/app/data/pr_computation/ee/3ee9/3ee9.pr.out
profile	/app/data/saxs_computation/ee/3ee9/3ee9.dat

Structure of NS1 effector domain

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

Refinement Refinement

Diffraction experiment Diffraction