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- PDB-6sx2: dsRNA recognition by R38AK41A mutant of H7N1 NS1 RNA Binding Domain -

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Basic information

Entry
Database: PDB / ID: 6sx2
TitledsRNA recognition by R38AK41A mutant of 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 / H7N1 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 / 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
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: 1.9 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)29,98413
Polymers29,4254
Non-polymers5599
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-20 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.690, 102.038, 102.696
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: 8672.932 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.62 Å3/Da / Density % sol: 66.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 100mM sodium phosphate/citric acid, 200mM ammonium sulfate, 40% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.9→45.87 Å / Num. obs: 34557 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.023 / Rrim(I) all: 0.052 / Net I/σ(I): 16.3 / Num. measured all: 179050 / Scaling rejects: 8
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.25 / Num. unique obs: 2202 / CC1/2: 0.481 / Rpim(I) all: 0.591 / Rrim(I) all: 1.385 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SW8

6sw8


Resolution: 1.9→37.796 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.65
RfactorNum. reflection% reflection
Rfree0.1915 1707 4.95 %
Rwork0.1677 --
obs0.169 34486 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.79 Å2 / Biso mean: 50.1329 Å2 / Biso min: 24.18 Å2
Refinement stepCycle: final / Resolution: 1.9→37.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 798 36 158 2109
Biso mean--56.67 49.76 -
Num. residues----182
LS refinement shellResolution: 1.9001→1.956 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3584 124 -
Rwork0.3569 2716 -
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)
14.2593-0.6323-0.55722.4393-1.20243.46830.18270.12680.02760.0072-0.15260.3287-0.1382-0.2091-0.02560.22280.02150.01990.35030.01040.28396.4373-17.696-8.6255
22.54811.77160.12558.34321.83383.08470.09940.34670.4196-0.8557-0.09840.4866-0.567-0.24310.05870.35760.10210.00650.38630.05180.33196.4411-10.4912-14.8553
33.4519-0.5991-0.42556.77131.68672.71360.0935-0.3082-0.2620.22610.1030.1398-0.1694-0.3211-0.10330.17810.00240.05460.32940.03930.29934.3504-21.9202-2.0835
44.0587-3.05620.98456.1662-1.55844.25880.17020.00490.50450.4485-0.1954-0.4368-0.72880.20360.04590.3269-0.04820.08210.3279-0.00770.353415.3909-8.16-4.0864
51.3822-0.1052-0.68598.0092-0.2112.24960.08350.1079-0.0332-0.4645-0.0714-0.8383-0.24170.24820.01330.2595-0.01130.03480.38120.06450.358420.7882-15.2752-8.1248
62.90294.49430.42958.43570.76716.11460.4423-1.2030.88870.8898-0.39830.5741-0.4091-0.0856-0.08650.5177-0.01180.12690.3218-0.0220.39811.3513-4.64131.6791
71.5797-0.45670.7651.8852-2.072.37080.1578-0.1871-0.1816-1.0624-0.3565-0.9709-0.3980.41490.68960.91610.00090.30040.39570.12530.704225.50363.4408-19.6238
81.97840.6269-0.06060.5721-0.93065.66750.5910.57730.1676-1.4048-0.4442-0.31030.6809-0.7595-0.2661.12970.0790.14390.47370.06220.448815.6242-9.2925-26.6816
94.40171.423-0.58455.4064-0.4324.90920.06940.5361-0.0827-1.496-0.2276-0.337-0.39520.49160.35950.69420.08830.1310.452-0.06150.444320.1242-27.3917-23.8946
105.7863-0.172-0.75690.6533-0.4366.070.4142-0.0924-0.0411-1.0111-0.4955-0.6301-0.14730.020.06870.62970.08420.16590.34590.01980.405318.4371-22.4261-24.6773
113.39432.5537-1.29734.6403-0.87562.7592-0.04960.73410.0056-1.2679-0.1497-0.72340.0594-0.16770.25731.06240.04950.260.43590.23960.712218.80382.1439-23.7488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 50 )A25 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 72 )A51 - 72
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 24 )B1 - 24
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 50 )B25 - 50
6X-RAY DIFFRACTION6chain 'B' and (resid 51 through 72 )B51 - 72
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 5 )C1 - 5
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 10 )C6 - 10
9X-RAY DIFFRACTION9chain 'C' and (resid 11 through 19 )C11 - 19
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 10 )D1 - 10
11X-RAY DIFFRACTION11chain 'D' and (resid 11 through 19 )D11 - 19

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