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- PDB-3m5r: Crystal Structure of Swine Flu Virus NS1 Effector Domain from H1N... -

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Basic information

Entry
Database: PDB / ID: 3m5r
TitleCrystal Structure of Swine Flu Virus NS1 Effector Domain from H1N1 Influenza A/California/07/2009
ComponentsNonstructural protein 1
KeywordsVIRAL PROTEIN / Swine Flu Virus / Influenza A H1N1 Subtype / Nonstructural Protein 1 / Effector domain / Viral immune evasion / Structural Genomics / NIAID / Center for Structural Genomics of Infectious Diseases / CSGID
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 / symbiont-mediated suppression of host gene expression / 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsFremont, D.H. / Yu, Y.Y.L. / Nelson, C.A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Swine Flu Virus NS1 Effector Domain from H1N1 Influenza A/California/07/2009
Authors: Fremont, D.H. / Yu, Y.Y.L. / Nelson, C.A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nonstructural protein 1
B: Nonstructural protein 1
D: Nonstructural protein 1
E: Nonstructural protein 1
F: Nonstructural protein 1
G: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)90,2306
Polymers90,2306
Non-polymers00
Water5,188288
1
A: Nonstructural protein 1
B: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)30,0772
Polymers30,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-13 kcal/mol
Surface area12200 Å2
2
D: Nonstructural protein 1
E: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)30,0772
Polymers30,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Nonstructural protein 1
G: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)30,0772
Polymers30,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.530, 70.795, 96.685
Angle α, β, γ (deg.)90.000, 110.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nonstructural protein 1


Mass: 15038.358 Da / Num. of mol.: 6 / Fragment: C-TERMINAL EFFECTOR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/07/2009 (H1N1) / Gene: NS1 / Plasmid: pET28A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: D2Y6Z6, UniProt: C3W611*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.7 M NaCl, 10% Ethanol and 0.1 M hexamine cobalt (III) chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 61983 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.061 / Χ2: 1.009 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.073.80.49661701.051100
2.07-2.153.80.38861420.951100
2.15-2.253.80.32761551.02299.9
2.25-2.373.80.20761911.018100
2.37-2.523.80.15661860.987100
2.52-2.713.80.11961691.011100
2.71-2.993.80.08862100.99100
2.99-3.423.80.06861771100
3.42-4.313.80.04462501.02999.9
4.31-1003.70.03663331.0399.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3F5T

3f5t


Resolution: 2→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.803 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1550 2.7 %RANDOM
Rwork0.207 ---
obs0.208 57329 91.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.955 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 91.98 Å2 / Biso mean: 40.529 Å2 / Biso min: 18.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.217 Å20 Å24.255 Å2
2--5.504 Å20 Å2
3----5.287 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 0 288 6136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085964
X-RAY DIFFRACTIONf_angle_d1.1048086
X-RAY DIFFRACTIONf_chiral_restr0.069932
X-RAY DIFFRACTIONf_plane_restr0.0041026
X-RAY DIFFRACTIONf_dihedral_angle_d14.72216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0790.3091270.2584659478677
2.079-2.1620.321430.2455121526485
2.162-2.260.3431370.2585206534386
2.26-2.380.2621520.2285302545488
2.38-2.5290.2691520.2255640579293
2.529-2.7240.2741670.2315759592695
2.724-2.9980.2621600.2285877603797
2.998-3.4320.2441740.2065992616699
3.432-4.3230.21660.1756052621899
4.323-500.2141720.196171634399

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