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- PDB-6sx0: Specific dsRNA recognition by wild type H7N1 NS1 RNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 6sx0
TitleSpecific dsRNA recognition by wild type H7N1 NS1 RNA-binding domain
Components
  • Non-structural protein 1
  • RNA (5'-R(*GP*GP*UP*AP*AP*CP*UP*GP*UP*UP*AP*CP*AP*GP*UP*UP*AP*CP*C)-3')
KeywordsVIRAL PROTEIN / INFLUENZA VIRUS / RNA-BINDING DOMAIN / RNA-PROTEIN COMPLEX
Function / homology
Function and homology information


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 / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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
RNA / RNA (> 10) / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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 24, 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

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 1
B: Non-structural protein 1
C: RNA (5'-R(*GP*GP*UP*AP*AP*CP*UP*GP*UP*UP*AP*CP*AP*GP*UP*UP*AP*CP*C)-3')
D: RNA (5'-R(*GP*GP*UP*AP*AP*CP*UP*GP*UP*UP*AP*CP*AP*GP*UP*UP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,69310
Polymers29,7144
Non-polymers1,9796
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-25 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.785, 60.397, 87.396
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


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: RNA chain RNA (5'-R(*GP*GP*UP*AP*AP*CP*UP*GP*UP*UP*AP*CP*AP*GP*UP*UP*AP*CP*C)-3')


Mass: 6039.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 100mM CHES, 30% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.75→43.26 Å / Num. obs: 27291 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 16.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.546 / Num. unique obs: 1481 / CC1/2: 0.571 / Rpim(I) all: 0.64 / Rrim(I) all: 1.675 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.3data scaling
PHASERphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SW8

6sw8


Resolution: 1.75→43.259 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 22.81
RfactorNum. reflection% reflection
Rfree0.2027 2555 4.98 %
Rwork0.1714 --
obs0.1731 27229 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.8 Å2 / Biso mean: 42.1301 Å2 / Biso min: 24.2 Å2
Refinement stepCycle: final / Resolution: 1.75→43.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 779 65 160 2104
Biso mean--65.17 45.91 -
Num. residues----179
LS refinement shellResolution: 1.75→1.7837 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3673 133 -
Rwork0.3365 2739 -
obs--100 %
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)
12.07670.74270.34722.0564-1.95295.50540.0869-0.0664-0.2341-0.0630.20470.15870.3255-0.19-0.280.2540.01-0.02360.24830.00430.4171-7.1719-9.443615.7615
20.9697-0.87530.514.0881-3.15344.27310.09770.216-0.217-0.4167-0.1275-0.08850.45580.3075-0.00680.2701-0.0136-0.00850.2332-0.0490.32930.0355-9.75769.2733
34.822-0.48853.77627.0548-2.57538.15970.3746-0.1253-0.8693-0.0210.09511.15620.1947-0.6761-0.40320.2446-0.0581-0.00010.36390.04260.4813-13.5391-11.417519.8642
42.9657-0.1688-2.78022.6894-0.21597.9028-0.07430.2937-0.0256-0.15980.07750.3461-0.0153-0.82450.00790.250.0008-0.04230.2684-0.00480.3624-8.92941.8858.2256
54.1707-4.110.00584.1318-0.16672.04850.0287-0.60540.14490.52330.2629-0.0424-0.72-0.4861-0.32080.45360.09010.07970.42520.03850.4229-8.1010.14526.673
61.0128-1.22891.77298.2088-8.30629.948-0.12930.0665-0.00270.282-0.2107-0.2225-0.45630.35890.3370.2478-0.0097-0.02480.2599-0.02570.3133-0.69645.877412.608
78.52435.4656-3.52234.8626-3.7065.4896-0.04270.0711-0.10210.01620.0941.07030.0201-0.8748-0.1510.2898-0.0039-0.10120.4437-0.00230.4865-15.66471.73244.6082
87.49456.5059-5.72997.9534-5.3694.4489-0.1346-0.3993-0.28740.0682-0.1987-0.29110.07860.43070.34270.3406-0.03450.00620.33070.04080.24818.72448.7378-0.7616
97.7368-4.09332.51128.1475-2.2247.0825-0.6128-0.2311-0.56510.37360.4478-0.0787-0.01030.89340.23480.36930.04570.0010.51290.01080.387312.548-5.08328.1477
105.49181.2243-2.83256.6857-3.99196.296-0.02460.11530.0380.0954-0.1733-0.66970.22810.75340.13020.24080.02-0.08750.37960.0080.289511.6035-3.335826.9868
115.2141-1.71325.79093.6179-2.6969.89790.02240.2919-0.3276-0.03480.24790.0319-0.15560.8165-0.29190.319-0.0273-0.01690.3799-0.0230.301312.313-10.399726.3141
125.0276-2.70234.84596.42560.25347.0002-0.37760.49050.2415-0.38590.58390.0777-0.25740.5532-0.150.3118-0.05880.00760.49070.05110.381411.68642.817716.0253
134.02422.26385.91823.71673.48728.706-0.12130.5942-0.2282-0.41140.3766-0.744-0.62871.4274-0.32220.4017-0.11720.15370.6141-0.00270.489417.0369-1.77921.7379
142.35550.2972-1.31537.30683.44842.61650.2050.60960.339-0.8144-0.256-0.19360.0657-0.06990.04660.42660.0220.03290.42570.03510.2942.67583.5623-8.008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )A2 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 50 )A25 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 71 )A51 - 71
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 24 )B1 - 24
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 29 )B25 - 29
6X-RAY DIFFRACTION6chain 'B' and (resid 30 through 50 )B30 - 50
7X-RAY DIFFRACTION7chain 'B' and (resid 51 through 71 )B51 - 71
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 5 )C1 - 5
9X-RAY DIFFRACTION9chain 'C' and (resid 6 through 10 )C6 - 10
10X-RAY DIFFRACTION10chain 'C' and (resid 11 through 19 )C11 - 19
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 5 )D1 - 5
12X-RAY DIFFRACTION12chain 'D' and (resid 6 through 10 )D6 - 10
13X-RAY DIFFRACTION13chain 'D' and (resid 11 through 15 )D11 - 15
14X-RAY DIFFRACTION14chain 'D' and (resid 16 through 19 )D16 - 19

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