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- PDB-3kwi: X-ray structure of NS1 effector domain W187Y mutant -

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Basic information

Entry
Database: PDB / ID: 3kwi
TitleX-ray structure of NS1 effector domain W187Y mutant
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / influenza / NS1 / effector domain / Alternative splicing / Host cytoplasm / Host nucleus / Host-virus interaction / Interferon antiviral system evasion / RNA-binding / Suppressor of RNA silencing
Function / homology
Function and homology information


symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response ...symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell nucleus / 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
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsXia, S. / Robertus, J.D.
CitationJournal: Arch.Biochem.Biophys. / Year: 2010
Title: X-ray structures of NS1 effector domain mutants.
Authors: Xia, S. / Robertus, J.D.
History
DepositionDec 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)32,0292
Polymers32,0292
Non-polymers00
Water1,49583
1
A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)16,0141
Polymers16,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)16,0141
Polymers16,0141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.991, 60.236, 132.655
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 Non-structural protein 1 / NS1 / NS1A


Mass: 16014.423 Da / Num. of mol.: 2 / Fragment: NS1 effector domain / Mutation: W187Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: influenza A/Udorn/72 virus / Gene: NS / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P03495
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5
Details: 0.3M magnesium formate and 0.1M Bis-Tris , pH 5.5, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 22, 2009 / Details: VARIMAX
RadiationMonochromator: VARIMAX OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. all: 19795 / Num. obs: 18310 / % possible obs: 99 % / Redundancy: 10 % / Rmerge(I) obs: 0.048 / Rsym value: 0.041 / Net I/σ(I): 51.4
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 62.2 / Num. unique all: 1771 / Rsym value: 0.242 / % possible all: 90.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EE9

3ee9


Resolution: 2.21→36.12 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.059 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25762 983 5.1 %RANDOM
Rwork0.22184 ---
all0.22362 19795 --
obs0.22362 18310 97.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.428 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2--0.93 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.21→36.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 0 83 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221923
X-RAY DIFFRACTIONr_bond_other_d00.021828
X-RAY DIFFRACTIONr_angle_refined_deg1.0031.9762603
X-RAY DIFFRACTIONr_angle_other_deg0.51634243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29224.26882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74215353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0071513
X-RAY DIFFRACTIONr_chiral_restr0.0580.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212092
X-RAY DIFFRACTIONr_gen_planes_other00.02373
X-RAY DIFFRACTIONr_mcbond_it1.2331190
X-RAY DIFFRACTIONr_mcbond_other0.2213486
X-RAY DIFFRACTIONr_mcangle_it2.3451935
X-RAY DIFFRACTIONr_scbond_it3.5397733
X-RAY DIFFRACTIONr_scangle_it5.85111668
LS refinement shellResolution: 2.213→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 54 -
Rwork0.292 1155 -
obs--83.26 %

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