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- PDB-6nu0: Solution NMR structure of 1918 NS1 effector domain -

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Basic information

Entry
Database: PDB / ID: 6nu0
TitleSolution NMR structure of 1918 NS1 effector domain
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / Virulence factor / Hijack host proteins
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 / virus-mediated perturbation of host defense response / 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) / Nucleotidyltransferase; domain 5 / S15/NS1, RNA-binding / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1 / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodSOLUTION NMR / simulated annealing
AuthorsShen, Q. / Cho, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)1R01GM127723-01A1 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: The structure and conformational plasticity of the nonstructural protein 1 of the 1918 influenza A virus.
Authors: Shen, Q. / Cho, J.H.
History
DepositionJan 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)26,0731
Polymers26,0731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Non-structural protein 1 / NS1


Mass: 26073.020 Da / Num. of mol.: 1 / Mutation: W187R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NS1, NS / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z5CYV0, UniProt: Q99AU3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic23D HNCO
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D H(CCO)NH
161isotropic13D 1H-15N TOCSY
171isotropic23D 1H-15N NOESY
182isotropic13D 1H-13C NOESY aliphatic
192isotropic23D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.15 mM [U-99% 13C; U-99% 15N] NS1 effector domain, 20 mM sodium phosphate, 80 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2OSample190% H2O/10% D2O
solution20.15 mM [U-99% 13C; U-99% 15N] NS1 effector domain, 20 mM sodium phosphate, 80 mM sodium chloride, 1 mM DTT, 100% D2OSample2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.15 mMNS1 effector domain[U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
80 mMsodium chloridenatural abundance1
1 mMDTTnatural abundance1
0.15 mMNS1 effector domain[U-99% 13C; U-99% 15N]2
20 mMsodium phosphatenatural abundance2
80 mMsodium chloridenatural abundance2
1 mMDTTnatural abundance2
Sample conditionsIonic strength: 80 mM / Label: Condition1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyNMRFAM-Sparky 1.3Goddardchemical shift assignment
SparkyNMRFAM-Sparky 1.3Goddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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