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- PDB-2zko: Structural basis for dsRNA recognition by NS1 protein of human in... -

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Basic information

Entry
Database: PDB / ID: 2zko
TitleStructural basis for dsRNA recognition by NS1 protein of human influenza virus A
Components
  • Non-structural protein 1
  • RNA (5'-R(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / dsRNA / protein-RNA interaction / Host-virus interaction / Interferon antiviral system evasion / Nucleus / RNA-binding / Suppressor of RNA silencing / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / symbiont-mediated suppression of host mRNA processing / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / NS1 Mediated Effects on Host Pathways / protein serine/threonine kinase inhibitor activity / RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity ...Inhibition of IFN-beta / Inhibition of PKR / Inhibition of Host mRNA Processing and RNA Silencing / symbiont-mediated suppression of host mRNA processing / Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host PKR/eIFalpha signaling / NS1 Mediated Effects on Host Pathways / protein serine/threonine kinase inhibitor activity / RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / Viral mRNA Translation / PKR-mediated signaling / ISG15 antiviral mechanism / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / RNA binding / identical protein 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 / Helix Hairpins / S15/NS1, RNA-binding / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYuan, Y.A.
CitationJournal: Cell Res. / Year: 2009
Title: Structural basis for dsRNA recognition by NS1 protein of influenza A virus
Authors: Cheng, A. / Wong, S.M. / Yuan, Y.A.
History
DepositionMar 26, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RNA (5'-R(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')
D: RNA (5'-R(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')
A: Non-structural protein 1
B: Non-structural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1056
Polymers29,9214
Non-polymers1842
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-52 kcal/mol
Surface area13550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.707, 57.218, 83.709
Angle α, β, γ (deg.)90.00, 105.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (5'-R(P*AP*GP*AP*CP*AP*GP*CP*AP*UP*UP*AP*UP*GP*CP*UP*GP*UP*CP*UP*UP*U)-3')


Mass: 6651.948 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 8308.460 Da / Num. of mol.: 2 / Fragment: residue 1-70
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: strain A/Puerto Rico/8/1934 H1N1 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/RIL / References: UniProt: P03496
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Magnesium acetate, MES, Ammonium sulfate, ATP, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Magnesium acetate11
2MES11
3Ammonium sulfate11
4ATPAdenosine triphosphate11
5HOH11
6Magnesium acetate12
7MES12
8Ammonium sulfate12
9ATPAdenosine triphosphate12
10HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 28868 / Num. obs: 28724 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rsym value: 0.077 / Net I/σ(I): 30.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.539 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AIL

1ail


Resolution: 1.7→40.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.901 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22965 1525 5 %RANDOM
Rwork0.1886 ---
obs0.19075 28723 99.32 %-
all-28868 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.048 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 884 12 205 2225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212132
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.252.4853062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7165138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.07822.06958
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86715218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9711518
X-RAY DIFFRACTIONr_chiral_restr0.0630.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021274
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.2975
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2830.21457
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7341.5704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1521112
X-RAY DIFFRACTIONr_scbond_it1.47731830
X-RAY DIFFRACTIONr_scangle_it2.2694.51950
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 99 -
Rwork0.225 1976 -
obs--91.85 %
Refinement TLS params.Method: refined / Origin x: 15.1892 Å / Origin y: 5.5864 Å / Origin z: 16.8853 Å
111213212223313233
T-0.0563 Å2-0.0247 Å20.0013 Å2--0.1045 Å20.0031 Å2---0.069 Å2
L2.0521 °2-0.1166 °20.1321 °2-0.5976 °20.0291 °2--1.2758 °2
S0.0494 Å °-0.226 Å °-0.0012 Å °0.059 Å °-0.0168 Å °-0.004 Å °-0.0035 Å °-0.0111 Å °-0.0327 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC1 - 704 - 73
2X-RAY DIFFRACTION1BD1 - 704 - 73
3X-RAY DIFFRACTION1CA1 - 211 - 21
4X-RAY DIFFRACTION1DB1 - 211 - 21

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