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

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Basic information

Entry
Database: PDB / ID: 3rvc
TitleEffector domain of NS1 from influenza A/PR/8/34 containing a W187A mutation
ComponentsNon-structural protein 1
KeywordsPROTEIN BINDING / Interferon Antagonist
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
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKerry, P.S. / Long, E. / Taylor, M.A. / Russell, R.J.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality.
Authors: Kerry, P.S. / Long, E. / Taylor, M.A. / Russell, R.J.
History
DepositionMay 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)16,8761
Polymers16,8761
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.992, 102.773, 67.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-74-

HOH

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Components

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


Mass: 16875.506 Da / Num. of mol.: 1 / Mutation: W187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Puerto Rico/8/1934 H1N1 / Gene: NS / Production host: Escherichia coli (E. coli) / References: UniProt: P03496
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.64 Å3/Da / Density % sol: 25.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Bis Tris, 0.2M NaCl, 22% PEG 3350, 20mM Xylitol, 40mM thieno[2.3-b]pyridin-2-ylmethanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→18.098 Å / Num. all: 9857 / Num. obs: 9857 / % possible obs: 100 % / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.83 Å

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→18 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 23.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 950 9.98 %
Rwork0.195 --
obs0.1999 9517 89.17 %
all-10673 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.506 Å2 / ksol: 0.409 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9469 Å2-0 Å2-0 Å2
2---2.6244 Å20 Å2
3---0.6775 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 0 81 999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007932
X-RAY DIFFRACTIONf_angle_d1.031262
X-RAY DIFFRACTIONf_dihedral_angle_d13.657350
X-RAY DIFFRACTIONf_chiral_restr0.07150
X-RAY DIFFRACTIONf_plane_restr0.004161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.89460.3122810.234703X-RAY DIFFRACTION53
1.8946-2.01320.26661190.20341069X-RAY DIFFRACTION78
2.0132-2.16840.271430.19361313X-RAY DIFFRACTION98
2.1684-2.38620.23431450.19771328X-RAY DIFFRACTION98
2.3862-2.73040.27551470.20221344X-RAY DIFFRACTION98
2.7304-3.43620.21371530.18751358X-RAY DIFFRACTION98
3.4362-18.09890.2441620.19261452X-RAY DIFFRACTION100

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