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- PDB-6nrl: X-ray structure of H6N6-NS1 delta(80-84) R38A K41A E71G mutant -

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Basic information

Entry
Database: PDB / ID: 6nrl
TitleX-ray structure of H6N6-NS1 delta(80-84) R38A K41A E71G 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 / 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) / 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: 3.2 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
DepositionJan 23, 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)21,9991
Polymers21,9991
Non-polymers00
Water1267
1
A: Non-structural protein 1

A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)43,9982
Polymers43,9982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area1590 Å2
ΔGint-4 kcal/mol
Surface area23430 Å2
MethodPISA
2
A: Non-structural protein 1

A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)43,9982
Polymers43,9982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area1880 Å2
ΔGint-7 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.190, 105.190, 80.210
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: 21999.168 Da / Num. of mol.: 1 / Mutation: delta80-84, E71G, R38A, K41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2Y234
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium citrate, 0.1 M Tris hydrochloride pH 8.5, and 30% (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: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999949 Å / Relative weight: 1
ReflectionResolution: 3.2→34.432 Å / Num. obs: 4652 / % possible obs: 99.61 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 2.1
Reflection shellResolution: 3.2→3.315 Å / Rmerge(I) obs: 0.163 / Num. unique obs: 661 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OPH

4oph


Resolution: 3.2→34.432 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2593 241 5.19 %
Rwork0.243 --
obs0.2442 4641 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→34.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1525 0 0 7 1532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041549
X-RAY DIFFRACTIONf_angle_d0.9012092
X-RAY DIFFRACTIONf_dihedral_angle_d6.492939
X-RAY DIFFRACTIONf_chiral_restr0.048238
X-RAY DIFFRACTIONf_plane_restr0.005272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2005-4.03130.32891170.27462131X-RAY DIFFRACTION100
4.0313-34.43350.23741240.23252269X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.3361 Å / Origin y: -40.2848 Å / Origin z: -1.461 Å
111213212223313233
T0.8108 Å20.0623 Å2-0.0975 Å2-0.899 Å2-0.0051 Å2--1.0079 Å2
L1.8962 °21.426 °2-1.7928 °2-1.4612 °2-2.1673 °2--5.1182 °2
S0.2962 Å °-0.1971 Å °0.2544 Å °0.3761 Å °0.0716 Å °0.5128 Å °-1.2938 Å °0.4253 Å °-0.0014 Å °
Refinement TLS groupSelection details: all

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