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- PDB-6o01: X-ray structure of H5N1-NS1 R38A K41A G71E mutant -

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Basic information

Entry
Database: PDB / ID: 6o01
TitleX-ray structure of H5N1-NS1 R38A K41A G71E 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 / 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 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
DepositionFeb 14, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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)24,3251
Polymers24,3251
Non-polymers00
Water1267
1
A: Non-structural protein 1

A: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)48,6502
Polymers48,6502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-5/61
Buried area1800 Å2
ΔGint-13 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.570, 105.570, 82.400
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: 24324.842 Da / Num. of mol.: 1 / Mutation: G71E, 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: Q6QT26
#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: 2.73 Å3/Da / Density % sol: 54.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Sodium acetate trihydrate and 0.1 M Tris hydrochloride pH 8.5

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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: Jan 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999949 Å / Relative weight: 1
ReflectionResolution: 3→30.604 Å / Num. obs: 5785 / % possible obs: 99.71 % / Redundancy: 19.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 2.1
Reflection shellResolution: 3→3.107 Å / Rmerge(I) obs: 1.64 / Num. unique obs: 566

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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: 3F5T

3f5t


Resolution: 3→30.604 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 280 4.84 %
Rwork0.2293 --
obs0.2316 5786 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→30.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 0 7 1520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051536
X-RAY DIFFRACTIONf_angle_d0.8442077
X-RAY DIFFRACTIONf_dihedral_angle_d2.011934
X-RAY DIFFRACTIONf_chiral_restr0.046242
X-RAY DIFFRACTIONf_plane_restr0.005269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.77860.35321350.25052685X-RAY DIFFRACTION100
3.7786-30.6060.24711450.21882821X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.4249 Å / Origin y: 64.8495 Å / Origin z: -11.947 Å
111213212223313233
T0.4214 Å2-0.1458 Å2-0.1064 Å2-0.3403 Å20.0901 Å2--0.3277 Å2
L2.0173 °20.3863 °2-1.7875 °2-0.3436 °20.02 °2--1.9997 °2
S0.3181 Å °0.5218 Å °0.6699 Å °-0.2267 Å °0.1323 Å °0.0358 Å °-0.2093 Å °-1.1888 Å °0.5136 Å °
Refinement TLS groupSelection details: all

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