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- PDB-3p39: Crystal structure of the NS1 effector domain W182A mutant from in... -

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Basic information

Entry
Database: PDB / ID: 3p39
TitleCrystal structure of the NS1 effector domain W182A mutant from influenza A/Vietnam/1203/2004 (H5N1) virus
ComponentsNonstructural protein 1
KeywordsVIRAL 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 / 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 / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 1
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsChen, S. / Xiao, Y.B. / Bricogne, G. / Sharff, A.J. / Hilgenfeld, R.
CitationJournal: To be Published
Title: X-ray structures of the NS1 effector domain from highly pathogenic influenza A/Vietnam/1203/2004 (H5N1) virus
Authors: Chen, S. / Xiao, Y.B. / Bricogne, G. / Sharff, A.J. / Hilgenfeld, R.
History
DepositionOct 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,0826
Polymers98,0826
Non-polymers00
Water1,802100
1
A: Nonstructural protein 1
B: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)32,6942
Polymers32,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nonstructural protein 1
D: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)32,6942
Polymers32,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Nonstructural protein 1

F: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)32,6942
Polymers32,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
4
F: Nonstructural protein 1

E: Nonstructural protein 1


Theoretical massNumber of molelcules
Total (without water)32,6942
Polymers32,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
Unit cell
Length a, b, c (Å)113.489, 113.489, 197.441
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Nonstructural protein 1


Mass: 16346.924 Da / Num. of mol.: 6 / Fragment: C-terminal effector domain, UNP residues 73-215 / Mutation: W182A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/environment/Viet Nam/1203/2004(H5N1) / Gene: NS1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: D1LP63
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.1M Bicine, 1.8 M MgCl2, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 19, 2010
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.14→37.3 Å / Num. all: 22045 / Num. obs: 21988 / % possible obs: 94.61 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 51.83 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 16.8
Reflection shellResolution: 3.14→3.29 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.2 / % possible all: 46.5

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.0refinement
PDB_EXTRACT3.1data extraction
MxCuBEGUIdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
BUSTER2.11.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3P31

3p31


Resolution: 3.14→37.3 Å / Cor.coef. Fo:Fc: 0.8882 / Cor.coef. Fo:Fc free: 0.856 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1128 5.13 %RANDOM
Rwork0.2069 ---
obs0.2085 21988 94.61 %-
all-22045 --
Displacement parametersBiso mean: 47.86 Å2
Baniso -1Baniso -2Baniso -3
1-10.3016 Å20 Å20 Å2
2--10.3016 Å20 Å2
3----20.6032 Å2
Refine analyzeLuzzati coordinate error obs: 0.614 Å
Refinement stepCycle: LAST / Resolution: 3.14→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 0 100 5900
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2139SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes144HARMONIC2
X-RAY DIFFRACTIONt_gen_planes831HARMONIC5
X-RAY DIFFRACTIONt_it5890HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion813SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6437SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5890HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7949HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion20.87
LS refinement shellResolution: 3.14→3.29 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2599 111 5.38 %
Rwork0.2447 1954 -
all0.2455 2065 -
obs--94.61 %

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