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- PDB-3kwg: X-ray structure of NS1 effector domain W187A mutant -

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Basic information

Entry
Database: PDB / ID: 3kwg
TitleX-ray structure of NS1 effector domain W187A mutant
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / influenza / NS1 / effector domain / 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 mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / signaling receptor inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression ...symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / signaling receptor inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / signaling receptor binding / 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)31,8452
Polymers31,8452
Non-polymers00
Water4,143230
1
A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)15,9221
Polymers15,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)15,9221
Polymers15,9221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Non-structural protein 1

B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)31,8452
Polymers31,8452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area1260 Å2
ΔGint-10 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.784, 48.193, 154.687
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: 15922.325 Da / Num. of mol.: 2 / Fragment: NS1 effector domain / Mutation: W187A
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.: 230 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.5
Details: 0.3M magnesium formate, 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: Jul 25, 2008 / 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→30 Å / Num. all: 18544 / Num. obs: 17384 / Redundancy: 13.4 % / Rmerge(I) obs: 0.061 / Rsym value: 0.042 / Net I/σ(I): 79
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 12 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 23.9 / Num. unique all: 1710 / % possible all: 92.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EE9

3ee9


Resolution: 2.21→28.35 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.618 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23304 941 5.1 %RANDOM
Rwork0.18703 ---
all0.18944 18544 --
obs0.18944 17384 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.443 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--0.68 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.21→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 0 230 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222030
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.9752745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1095253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9724.41986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80315374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9481514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021490
X-RAY DIFFRACTIONr_nbd_refined0.1880.2880
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2205
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.221
X-RAY DIFFRACTIONr_mcbond_it1.56831317
X-RAY DIFFRACTIONr_mcangle_it2.55552061
X-RAY DIFFRACTIONr_scbond_it4.0357811
X-RAY DIFFRACTIONr_scangle_it6.05511684
LS refinement shellResolution: 2.214→2.272 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 64 -
Rwork0.202 1232 -
obs-1710 95.86 %

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