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- PDB-6oqe: X-ray structure of H6N6-NS1 delta(80-84) R38A K41A mutant -

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Basic information

Entry
Database: PDB / ID: 6oqe
TitleX-ray structure of H6N6-NS1 delta(80-84) R38A K41A mutant
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / Protein
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 virus non-structural protein, effector domain / 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 / Helix Hairpins / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich ...Influenza virus non-structural protein, effector domain / 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 / Helix Hairpins / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.899 Å
AuthorsMitra, S. / Kumar, D. / Hu, L. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch FoundationQ1279 United States
CitationJournal: J.Virol. / Year: 2019
Title: Influenza A Virus Protein NS1 Exhibits Strain-Independent Conformational Plasticity.
Authors: Mitra, S. / Kumar, D. / Hu, L. / Sankaran, B. / Moosa, M.M. / Rice, A.P. / Ferreon, J.C. / Ferreon, A.C.M. / Prasad, B.V.V.
History
DepositionApr 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)25,9581
Polymers25,9581
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.156, 106.156, 79.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Non-structural protein 1 / NS1


Mass: 25957.619 Da / Num. of mol.: 1 / Mutation: R38A, K41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NS1, NS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q20NS3

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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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Sodium citrate tribasic dehydrate, 0.1 M Tris hydrochloride pH 7.0, and 15% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999949 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999949 Å / Relative weight: 1
ReflectionResolution: 3.899→28.612 Å / Num. obs: 2536 / % possible obs: 95.2 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 12.8
Reflection shellResolution: 3.899→4 Å / Rmerge(I) obs: 0.94 / Num. unique obs: 196 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(dev_3406: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OPH

4oph


Resolution: 3.899→28.612 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.36
RfactorNum. reflection% reflection
Rfree0.2943 126 5 %
Rwork0.2448 --
obs0.2473 2519 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.899→28.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1375 0 0 0 1375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031394
X-RAY DIFFRACTIONf_angle_d0.5591891
X-RAY DIFFRACTIONf_dihedral_angle_d6.633844
X-RAY DIFFRACTIONf_chiral_restr0.041227
X-RAY DIFFRACTIONf_plane_restr0.004244
LS refinement shellResolution: 3.899→28.6131 Å
RfactorNum. reflection% reflection
Rfree0.2943 126 -
Rwork0.2448 2393 -
obs--94 %
Refinement TLS params.Method: refined / Origin x: 60.6795 Å / Origin y: 50.1299 Å / Origin z: -42.86 Å
111213212223313233
T1.1372 Å20.1869 Å2-0.2035 Å2-0.8909 Å2-0.2712 Å2--1.2368 Å2
L2.8801 °22.44 °2-0.7119 °2--0.5264 °2-0.4454 °2--1.8811 °2
S0.6352 Å °-0.4271 Å °0.6122 Å °0.6407 Å °0.7379 Å °1.2757 Å °-0.693 Å °0.6201 Å °0.5144 Å °
Refinement TLS groupSelection details: all

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