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- PDB-5by1: H18 Bat Influenza NS1 RNA Binding Domain -

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Basic information

Entry
Database: PDB / ID: 5by1
TitleH18 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 / : / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host gene expression / 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
DI(HYDROXYETHYL)ETHER / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.751 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 1.3Jan 10, 2024Group: 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

Downloads & links

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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)19,2124
Polymers18,8682
Non-polymers3442
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-14 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.661, 56.834, 39.814
Angle α, β, γ (deg.)90.000, 97.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Non-structural protein 1 / NS1


Mass: 9433.925 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/flat-faced bat/Peru/033/2010(H18N11))
Gene: NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: U5N1D7
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.82 Å3/Da / Density % sol: 32.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6.5 / Details: 0.2M Na Acetate, 0.1M MES pH 6.5, 30% PEG400

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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 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 13038 / % possible obs: 94.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.058 / Χ2: 2.268 / Net I/av σ(I): 33.261 / Net I/σ(I): 14.6 / Num. measured all: 41172
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.781.80.4164022.08557.8
1.78-1.811.90.4144761.85368.6
1.81-1.852.30.4045511.9482.2
1.85-1.892.70.3756382.08593.3
1.89-1.933.20.3146782.013100
1.93-1.973.20.2786702.15499.6
1.97-2.023.30.2166912.032100
2.02-2.073.20.1656802.20299.9
2.07-2.143.30.1396762.296100
2.14-2.23.40.1187022.54699.9
2.2-2.283.40.1066682.37799.9
2.28-2.373.30.0856922.197100
2.37-2.483.40.086812.323100
2.48-2.613.40.0716842.145100
2.61-2.783.40.066972.044100
2.78-2.993.40.0496821.80699.7
2.99-3.293.50.0436871.82999.7
3.29-3.773.40.046862.00399.6
3.77-4.743.40.0466932.763100
4.74-303.20.0527044.01797.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.75 Å19.72 Å
Translation1.75 Å19.72 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
Starting model: 1AIL

1ail


Resolution: 1.751→19.716 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 1241 10.03 %
Rwork0.1601 11132 -
obs0.1649 12373 90.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.54 Å2 / Biso mean: 33.5906 Å2 / Biso min: 16.67 Å2
Refinement stepCycle: final / Resolution: 1.751→19.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 23 75 1230
Biso mean--48.41 41.19 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071171
X-RAY DIFFRACTIONf_angle_d0.9961561
X-RAY DIFFRACTIONf_chiral_restr0.034174
X-RAY DIFFRACTIONf_plane_restr0.006190
X-RAY DIFFRACTIONf_dihedral_angle_d15.383454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7506-1.82060.325800.239572980953
1.8206-1.90340.30281210.22861095121680
1.9034-2.00360.26051350.19321248138393
2.0036-2.1290.2031500.16971295144595
2.129-2.29320.21361510.16251321147297
2.2932-2.52360.2151480.16371329147797
2.5236-2.88770.21451490.16381356150598
2.8877-3.63450.22431510.15461365151699
3.6345-19.71710.17211560.14371394155099
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)
10.0582-0.042-0.06690.02490.02290.112-0.03210.1069-0.213-0.05950.0995-0.0617-0.18360.07760.00020.1995-0.00070.00190.2173-0.0130.23686.389839.02070.5244
20.1596-0.0078-0.14440.0659-0.00370.1299-0.1679-0.1336-0.25690.07850.0625-0.07590.18740.10030.00150.25640.01350.00540.249-0.00270.28759.235332.1698.289
30.12550.0736-0.0480.0454-0.00960.0551-0.12190.35390.0693-0.08260.17860.0472-0.0847-0.03960.00050.22510.00070.01520.20610.00450.19946.170243.3594-5.033
40.2041-0.0783-0.1850.04810.08560.1672-0.0564-0.0052-0.0680.12860.10330.1204-0.2219-0.04630.00020.21430.0179-0.020.2229-0.00210.18270.531544.51679.5991
50.119-0.15830.03880.23890.03470.147-0.0208-0.0347-0.02130.04730.05510.1104-0.2797-0.201-0.00010.241-0.01690.01450.1921-0.00760.22691.92644.813512.855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 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 4 through 30 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 74 )B0

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