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- PDB-3ee9: Structure of NS1 effector domain -

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Basic information

Entry
Database: PDB / ID: 3ee9
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 type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / 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 type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / 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: 2.14 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7844
Polymers27,5922
Non-polymers1922
Water2,450136
1
A: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8922
Polymers13,7961
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8922
Polymers13,7961
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.924, 61.456, 132.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 298 K / Method: batch / pH: 5.5
Details: 20% (w/v) PEG400, 0.1M CH3COONa (pH5.5), 0.1M MgSO4, Batch, 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 8, 2008 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→30 Å / Num. all: 19831 / Num. obs: 19831 / % possible obs: 87.7 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.066 / Χ2: 1.029 / Net I/σ(I): 28.48
Reflection shellResolution: 2.13→2.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.6 / Num. unique all: 661 / Χ2: 0.514 / % possible all: 29.7

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Processing

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

2gx9


Resolution: 2.14→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.832 / SU B: 4.685 / SU ML: 0.122 / SU R Cruickshank DPI: 0.212 / SU Rfree: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 956 5.1 %RANDOM
Rwork0.198 ---
obs0.199 18722 84.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.36 Å2 / Biso mean: 44.67 Å2 / Biso min: 19.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--1.17 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.14→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 10 143 2062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221954
X-RAY DIFFRACTIONr_bond_other_d0.0010.021344
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9722645
X-RAY DIFFRACTIONr_angle_other_deg0.81633281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83924.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22115358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4931514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02385
X-RAY DIFFRACTIONr_nbd_refined0.1920.2343
X-RAY DIFFRACTIONr_nbd_other0.1930.21361
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2936
X-RAY DIFFRACTIONr_nbtor_other0.0850.21055
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.25
X-RAY DIFFRACTIONr_mcbond_it2.25931571
X-RAY DIFFRACTIONr_mcbond_other0.3563483
X-RAY DIFFRACTIONr_mcangle_it2.84151941
X-RAY DIFFRACTIONr_scbond_it4.5187881
X-RAY DIFFRACTIONr_scangle_it6.17411704
LS refinement shellResolution: 2.142→2.198 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 26 -
Rwork0.232 459 -
all-485 -
obs--29.86 %

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