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- PDB-6sw8: Crystal structure of the NS1 (H7N1) RNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 6sw8
TitleCrystal structure of the NS1 (H7N1) RNA-binding domain
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / INFLUENZA VIRUS / RNA-BINDING DOMAIN / RNA BINDING PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / protein serine/threonine kinase inhibitor activity / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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) / Influenza non-structural protein (NS1) / S15/NS1, RNA-binding
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.933 Å
AuthorsCoste, F. / Wacquiez, A. / Marc, D. / Castaing, B.
CitationJournal: Viruses / Year: 2020
Title: Structure and Sequence Determinants Governing the Interactions of RNAs with Influenza A Virus Non-Structural Protein NS1.
Authors: Wacquiez, A. / Coste, F. / Kut, E. / Gaudon, V. / Trapp, S. / Castaing, B. / Marc, D.
History
DepositionSep 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0337
Polymers17,6342
Non-polymers3985
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint1 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.827, 83.827, 68.527
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Non-structural protein 1 / NS1


Mass: 8817.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/turkey/Italy/977/1999(H7N1))
Strain: A/turkey/Italy/977/1999(H7N1) / Gene: ns1, NS, NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1PST0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.14 Å3/Da / Density % sol: 70.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12M (Diethylene glycol, Triethylene glycol, Tetraethylene glycol, Pentaethylene glycol) + 0.1M (Sodium HEPES, MOPS) + 37.5% (MPD, PEG 1000, PEG 3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98009 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 1.93→49.832 Å / Num. obs: 21170 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 42.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.9
Reflection shellResolution: 1.93→1.97 Å / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 21170 / CC1/2: 0.704

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H5N

5h5n


Resolution: 1.933→49.832 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.28
RfactorNum. reflection% reflection
Rfree0.1932 977 4.62 %
Rwork0.1755 --
obs0.1763 21170 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.85 Å2 / Biso mean: 54.5362 Å2 / Biso min: 29.11 Å2
Refinement stepCycle: final / Resolution: 1.933→49.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1163 0 26 66 1255
Biso mean--75.5 51.16 -
Num. residues----146
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)
16.09281.61370.59248.0147-2.90486.91280.00430.31540.3422-0.35480.35921.23110.0953-0.4929-0.34810.2737-0.0831-0.03630.35240.01190.399624.9599-23.9772-1.011
24.75963.7501-2.83865.7415-5.16676.8228-0.93760.9225-0.0494-1.91490.609-0.51030.4653-0.58720.27040.5766-0.184-0.05760.59860.0030.408927.4299-26.8016-9.2266
34.9642.0251.6335.18420.18694.45590.334-0.90830.48650.9415-0.45780.965-0.0749-0.86220.24320.5134-0.10270.11370.4672-0.00240.498323.1313-27.33288.2572
43.8481.75940.13564.7304-2.88966.88920.26430.03610.36130.2632-0.09250.4619-0.49960.1156-0.31750.3202-0.05420.06960.2932-0.02960.365332.7822-15.8682.129
52.01272.1438-0.86954.736-2.18613.4210.1634-0.0890.33980.36410.07380.2864-0.4216-0.0665-0.13770.3839-0.02690.04340.318-0.01040.326633.5801-16.35561.8359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 29 )B1 - 29
2X-RAY DIFFRACTION2chain 'B' and (resid 30 through 50 )B30 - 50
3X-RAY DIFFRACTION3chain 'B' and (resid 51 through 73 )B51 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 25 )A1 - 25
5X-RAY DIFFRACTION5chain 'A' and (resid 26 through 73 )A26 - 73

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