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- PDB-3o9u: Effector domain of influenza A/PR/8/34 NS1 -

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Basic information

Entry
Database: PDB / ID: 3o9u
TitleEffector domain of influenza A/PR/8/34 NS1
ComponentsNonstructural protein 1
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / symbiont-mediated suppression of host mRNA processing / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / NS1 Mediated Effects on Host Pathways / RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity ...Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / symbiont-mediated suppression of host mRNA processing / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / NS1 Mediated Effects on Host Pathways / RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity / Viral mRNA Translation / PKR-mediated signaling / ISG15 antiviral mechanism / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / host cell nucleus / RNA binding / identical protein binding
Similarity search - Function
Influenza virus non-structural protein, effector domain / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1 / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKerry, P.S. / Lewis, A. / Hale, B.G. / Hass, C. / Taylor, M.A. / Randall, R.E. / Russell, R.J.M.
CitationJournal: Plos One / Year: 2011
Title: A Transient Homotypic Interaction Model for the Influenza A Virus NS1 Protein Effector Domain.
Authors: Kerry, P.S. / Ayllon, J. / Taylor, M.A. / Hass, C. / Lewis, A. / Garcia-Sastre, A. / Randall, R.E. / Hale, B.G. / Russell, R.J.
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Nonstructural protein 1
A: Nonstructural protein 1
C: Nonstructural protein 1
D: Nonstructural protein 1
E: Nonstructural protein 1
F: Nonstructural protein 1
G: Nonstructural protein 1
H: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)135,9258
Polymers135,9258
Non-polymers00
Water00
1
B: Nonstructural protein 1
E: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)33,9812
Polymers33,9812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nonstructural protein 1
C: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)33,9812
Polymers33,9812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Nonstructural protein 1
G: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)33,9812
Polymers33,9812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Nonstructural protein 1
H: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)33,9812
Polymers33,9812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.124, 114.124, 199.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 89:202 )
211CHAIN A AND (RESSEQ 89:202 )
311CHAIN C AND (RESSEQ 89:202 )
411CHAIN D AND (RESSEQ 89:202 )
511CHAIN E AND (RESSEQ 89:202 )
611CHAIN F AND (RESSEQ 89:202 )
711CHAIN G AND (RESSEQ 89:202 )
811CHAIN H AND (RESSEQ 89:202 )

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Components

#1: Protein
Nonstructural protein 1


Mass: 16990.639 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: C9S2D8, UniProt: P03496*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.37 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.2→19.87 Å / Num. obs: 23538

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.1_357) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→19.87 Å / σ(F): 1.89 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2221 1222 5.19 %
Rwork0.1745 --
obs0.1748 23538 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.271 Å2 / ksol: 0.261 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.7585 Å2-0 Å2-0 Å2
2--4.7585 Å20 Å2
3----9.5171 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7247 0 0 0 7247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087359
X-RAY DIFFRACTIONf_angle_d1.1659962
X-RAY DIFFRACTIONf_dihedral_angle_d13.82776
X-RAY DIFFRACTIONf_chiral_restr0.061182
X-RAY DIFFRACTIONf_plane_restr0.0031269
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B891X-RAY DIFFRACTIONPOSITIONAL
12A891X-RAY DIFFRACTIONPOSITIONAL0.045
13C891X-RAY DIFFRACTIONPOSITIONAL0.045
14D891X-RAY DIFFRACTIONPOSITIONAL0.046
15E891X-RAY DIFFRACTIONPOSITIONAL0.042
16F891X-RAY DIFFRACTIONPOSITIONAL0.041
17G891X-RAY DIFFRACTIONPOSITIONAL0.043
18H891X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.35940.3561360.28512643X-RAY DIFFRACTION89
3.3594-3.53550.28161440.24512776X-RAY DIFFRACTION94
3.5355-3.75560.23451390.21792804X-RAY DIFFRACTION95
3.7556-4.04330.24471800.19732791X-RAY DIFFRACTION94
4.0433-4.44590.20831350.16852836X-RAY DIFFRACTION95
4.4459-5.07960.18851760.14752801X-RAY DIFFRACTION94
5.0796-6.36380.2541550.16522839X-RAY DIFFRACTION95
6.3638-19.70870.16381430.12182813X-RAY DIFFRACTION94

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