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- PDB-2gx9: X-ray structure of influenza virus NS1 effector domain -

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Basic information

Entry
Database: PDB / ID: 2gx9
TitleX-ray structure of influenza virus NS1 effector domain
ComponentsNS1 Effector Domain
KeywordsTRANSCRIPTION / VIRUS/VIRAL PROTEIN / NS1 / Influenza / Effector Domain / alpha-helix beta-crescent / VIRUS-VIRAL PROTEIN 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 / virus-mediated perturbation of host defense response / host cell nucleus / RNA binding / identical protein 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
THIOCYANATE ION / Non-structural protein 1 / Non-structural protein 1
Similarity search - Component
Biological speciesunidentified influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.1 Å
AuthorsBornholdt, Z.A. / Prasad, B.V.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: X-ray structure of influenza virus NS1 effector domain.
Authors: Bornholdt, Z.A. / Prasad, B.V.
History
DepositionMay 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: struct / struct_conn ...struct / struct_conn / struct_ref_seq_dif / struct_site
Item: _struct.title / _struct_conn.pdbx_leaving_atom_flag ..._struct.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS1 Effector Domain
B: NS1 Effector Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6485
Polymers29,4742
Non-polymers1743
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.000, 59.000, 268.022
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein NS1 Effector Domain / Nonstructural protein NS1


Mass: 14736.932 Da / Num. of mol.: 2 / Fragment: NS1 Effector Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Strain: A/Puerto Rico/8/34 / Gene: Segment 8 - NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q71QT3, UniProt: Q6LD08*PLUS
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.96 Å3/Da / Density % sol: 68.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 200 mM NaSCN, 100 mM Hepes pH 6.8, 16% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97909 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28692 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: MAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
133.89721.53512.743S201
250.01618.50610.346S200.994
318.43617.21815.004S200.911
46.85115.7784.784S200.893
52.09316.33811.334S200.856
645.26213.5216.259S200.852
729.49619.60514.058S200.792
8-1.474.07611.931S200.536
94.86925.074-0.103S200.4
1022.86919.47713.896S200.371
1111.37412.69628.464S200.346
129.13523.31223.769S200.312
1339.62211.198-4.364S200.164
1416.60818.92112.41S200.153
1515.38616.66413.17S200.144
1643.69915.4063.42S200.144
177.69316.06210.659S200.125
1818.93434.87910.743S200.116
19-3.64417.28529.048S200.104
2017.50514.09711.915S200.091
2149.45917.08214.182S200.079
2232.60421.15916.215S200.036
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 33028
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.23-10078.60.719502
6.55-8.2366.40.854512
5.61-6.5566.10.843617
4.98-5.6163.10.885679
4.53-4.9861.60.887728
4.18-4.5360.80.893802
3.9-4.18630.869863
3.67-3.962.30.88910
3.47-3.6760.30.879950
3.31-3.4764.30.861032
3.16-3.3161.90.8611069
3.04-3.1664.20.8351104
2.93-3.0462.50.8281121
2.82-2.9364.90.8011186
2.73-2.8263.40.8161222
2.65-2.7366.30.7941253
2.57-2.6563.40.7821272
2.5-2.5768.40.7681338
2.44-2.564.20.7771345
2.38-2.4467.40.7591381
2.33-2.3870.80.7471434
2.27-2.3368.40.7271422
2.23-2.2772.70.7211512
2.18-2.2372.20.6991497
2.14-2.1873.80.7061543
2.1-2.1477.20.6981544
2.06-2.176.80.6861618
2-2.0679.10.632572

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT2data extraction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.179 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.137
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1432 5 %RANDOM
Rwork0.206 ---
all0.207 ---
obs0.207 28692 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.881 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2--1.18 Å20 Å2
3----2.36 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 9 270 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221989
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9732689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.64223.97683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15615363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.121516
X-RAY DIFFRACTIONr_chiral_restr0.0770.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021452
X-RAY DIFFRACTIONr_nbd_refined0.2330.2889
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.220
X-RAY DIFFRACTIONr_mcbond_it0.8291.51246
X-RAY DIFFRACTIONr_mcangle_it1.61422013
X-RAY DIFFRACTIONr_scbond_it2.6353743
X-RAY DIFFRACTIONr_scangle_it4.3264.5676
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 99 -
Rwork0.224 1940 -
obs-2039 99.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.44070.3464-3.01120.8924-0.94922.6314-0.0741-0.30640.0970.12120.0312-0.0645-0.0620.04570.0429-0.19790.0227-0.02820.1911-0.0088-0.112639.421419.47817.0457
22.1810.17750.76550.8143-0.01221.2415-0.0627-0.1129-0.04070.01840.052-0.0154-0.08140.03650.0107-0.18720.0239-0.00290.1479-0.02-0.101812.04120.879715.9008
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA79 - 2051 - 127
22BB86 - 2078 - 129

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