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- PDB-5bxz: H17 Bat Influenza NS1 RNA Binding Domain -

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Basic information

Entry
Database: PDB / ID: 5bxz
TitleH17 Bat Influenza NS1 RNA Binding Domain
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / Immune Antagonist
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / virus-mediated perturbation of host defense response => GO:0019049 / host cell cytoplasm / host cell nucleus / RNA binding
Similarity search - Function
Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding / Helix Hairpins / S15/NS1, RNA-binding / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKerry, P.S. / Hale, B.G.
Funding support United Kingdom, Switzerland, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Swiss National Science Foundation31003A_159993 Switzerland
CitationJournal: J.Virol. / Year: 2015
Title: Novel Bat Influenza Virus NS1 Proteins Bind Double-Stranded RNA and Antagonize Host Innate Immunity.
Authors: Turkington, H.L. / Juozapaitis, M. / Kerry, P.S. / Aydillo, T. / Ayllon, J. / Garcia-Sastre, A. / Schwemmle, M. / Hale, B.G.
History
DepositionJun 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,0962
Polymers19,0962
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-17 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.675, 46.675, 60.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Non-structural protein 1 / NS1


Mass: 9547.918 Da / Num. of mol.: 2 / Fragment: UNP residues 1-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/little yellow-shouldered bat/Guatemala/153/2009(H17N10))
Gene: NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: H6QM79
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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

Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 25% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 4036 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.131 / Χ2: 2.408 / Net I/av σ(I): 24.969 / Net I/σ(I): 9.2 / Num. measured all: 28904
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.6470.4321932.04100
2.64-2.697.20.3931931.951100
2.69-2.7470.4092302.07100
2.74-2.87.20.3391862.158100
2.8-2.867.20.3031842.205100
2.86-2.9370.3022102.211100
2.93-37.20.2651962.159100
3-3.087.20.2642092.169100
3.08-3.177.10.192062.217100
3.17-3.287.30.1881792.246100
3.28-3.397.20.1662132.413100
3.39-3.537.30.1231982.632100
3.53-3.697.20.1241942.546100
3.69-3.887.20.1032222.62100
3.88-4.127.30.0921862.585100
4.12-4.447.40.0922102.666100
4.44-4.897.30.0791942.711100
4.89-5.597.30.0942122.652100
5.59-7.037.20.1062042.436100
7.03-306.70.0632173.3999.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.6 Å23.34 Å
Translation2.6 Å23.34 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→23.337 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2744 405 10.07 %
Rwork0.1733 3615 -
obs0.1837 4020 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 171.58 Å2 / Biso mean: 40.2537 Å2 / Biso min: 11.21 Å2
Refinement stepCycle: final / Resolution: 2.6→23.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 0 25 1146
Biso mean---31.77 -
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081141
X-RAY DIFFRACTIONf_angle_d1.1151533
X-RAY DIFFRACTIONf_chiral_restr0.039169
X-RAY DIFFRACTIONf_plane_restr0.005193
X-RAY DIFFRACTIONf_dihedral_angle_d16.438442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6002-2.97580.33431380.210311821320
2.9758-3.74670.30431320.179911961328
3.7467-23.33840.23171350.154112371372
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03330.0579-0.01770.5229-0.19940.0736-0.2387-0.2836-0.2097-0.4101-0.2853-0.089-0.447-0.2443-0.04760.25030.0224-0.02290.2490.00250.2203-19.71772.29391.5397
20.08880.3555-0.00231.19920.0980.0435-0.13790.49550.23380.45220.41610.601-0.05080.28320.06420.24120.03620.01240.23270.03110.2554-28.5673-0.13244.8239
30.61150.68730.17420.75270.23080.0462-0.32780.36050.1264-0.00730.08980.2762-0.03670.4897-0.12450.34630.01110.03630.3070.07390.1742-13.73135.9917-1.0167
40.51730.03760.09880.53980.16690.0486-0.1591-0.3968-0.6444-0.1880.0844-0.2598-0.2881-0.20390.00050.1372-0.00990.00780.17070.02060.1574-17.6518-10.82981.9053
50.0447-0.09740.06250.2342-0.0693-0.02090.09370.0891-0.16830.21020.0415-0.0637-0.01580.02050.00040.29430.02590.02620.1811-0.010.2856-17.7356-8.540812.4075
60.25870.1922-0.13042.1679-0.31970.0788-0.2055-0.0620.0142-0.47360.3598-0.48640.2857-0.43480.07650.217-0.0420.00670.2687-0.00990.185-14.5817-13.0481-3.6832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 26 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 51 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 71 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 25 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 51 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 52 through 71 )B0

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