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- PDB-3ee8: Structure of NS1 effector domain -

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Basic information

Entry
Database: PDB / ID: 3ee8
TitleStructure of NS1 effector domain
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / Zinc finger receptor / Alternative splicing / Cytoplasm / Host-virus interaction / Interferon antiviral system evasion / Nucleus / RNA-binding / Suppressor of RNA silencing
Function / homology
Function and homology information


symbiont-mediated suppression of host cytokine production / 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 innate immune response / 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 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 innate immune response / 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 / Resolution: 2.6 Å
AuthorsXia, S. / Monzingo, A.F. / Robertus, J.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of NS1A effector domain from the influenza A/Udorn/72 virus.
Authors: Xia, S. / Monzingo, A.F. / Robertus, J.D.
History
DepositionSep 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Non-structural protein 1
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)27,5922
Polymers27,5922
Non-polymers00
Water36020
1
A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)13,7961
Polymers13,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)13,7961
Polymers13,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.818, 74.028, 121.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 13795.988 Da / Num. of mol.: 2 / Fragment: Effector domain (UNP residues 84-205)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Udorn/307/1972(H3N2))
Strain: Udorn / Gene: NS / Plasmid: pET46 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P03495
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 12% (w/v) PEG3350, and 4% (v/v) Tacsimate (pH6.0), VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 23, 2008 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 7841 / Num. obs: 7841 / % possible obs: 85.7 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 3.7 / Num. unique all: 236 / % possible all: 26.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
MOLREPphasing
RefinementStarting model: PDBid: 2GX9

2gx9


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.17 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.772 / SU B: 14.408 / SU ML: 0.294 / SU Rfree: 0.412 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.284 352 4.6 %RANDOM
Rwork0.197 ---
obs0.201 7261 83.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.25 Å2 / Biso mean: 46.167 Å2 / Biso min: 13.19 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2---1.62 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 0 20 1943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221960
X-RAY DIFFRACTIONr_bond_other_d0.0010.021353
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.972654
X-RAY DIFFRACTIONr_angle_other_deg0.84633304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0185241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91324.09683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36715358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6021514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
X-RAY DIFFRACTIONr_nbd_refined0.2190.2426
X-RAY DIFFRACTIONr_nbd_other0.1940.21381
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2922
X-RAY DIFFRACTIONr_nbtor_other0.0880.21116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0640.22
X-RAY DIFFRACTIONr_mcbond_it2.30531568
X-RAY DIFFRACTIONr_mcbond_other0.3053491
X-RAY DIFFRACTIONr_mcangle_it3.04251969
X-RAY DIFFRACTIONr_scbond_it4.6757866
X-RAY DIFFRACTIONr_scangle_it6.82511685
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 5 -
Rwork0.235 141 -
all-146 -
obs--22.29 %

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