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- PDB-3o9r: Effector domain of NS1 from influenza A/PR/8/34 containing a W187... -

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Basic information

Entry
Database: PDB / ID: 3o9r
TitleEffector domain of NS1 from influenza A/PR/8/34 containing a W187A mutation
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 / protein serine/threonine kinase inhibitor activity / RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / protein serine/threonine kinase inhibitor activity / RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / Viral mRNA Translation / PKR-mediated signaling / ISG15 antiviral mechanism / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / 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: 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 ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nonstructural protein 1
B: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)33,7512
Polymers33,7512
Non-polymers00
Water3,711206
1
A: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)16,8761
Polymers16,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)16,8761
Polymers16,8761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.606, 70.109, 104.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nonstructural protein 1


Mass: 16875.506 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.4 %

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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: 2→28.245 Å / Num. obs: 15712

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.1_357) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.245 Å / SU ML: 0.27 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 807 5.14 %
Rwork0.196 --
obs0.1988 15712 90.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.128 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.066 Å20 Å2-0 Å2
2--3.4896 Å20 Å2
3----2.4237 Å2
Refinement stepCycle: LAST / Resolution: 2→28.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 0 206 2042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081864
X-RAY DIFFRACTIONf_angle_d1.0482524
X-RAY DIFFRACTIONf_dihedral_angle_d14.154700
X-RAY DIFFRACTIONf_chiral_restr0.071300
X-RAY DIFFRACTIONf_plane_restr0.004322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12460.3129950.22751751X-RAY DIFFRACTION66
2.1246-2.28860.27451150.2052466X-RAY DIFFRACTION91
2.2886-2.51880.26251620.19682530X-RAY DIFFRACTION94
2.5188-2.88290.25981560.19472586X-RAY DIFFRACTION95
2.8829-3.6310.23921410.17972698X-RAY DIFFRACTION98
3.631-28.24810.24121380.19522874X-RAY DIFFRACTION98

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