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- PDB-6dgk: Crystal Structure of the Non-Structural Protein 1 (NS1) effector ... -

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Basic information

Entry
Database: PDB / ID: 6dgk
TitleCrystal Structure of the Non-Structural Protein 1 (NS1) effector domain W187A mutant from the A/Brevig Mission/1/1918 (H1N1) strain of Influenza A Virus
ComponentsNon-structural protein 1
KeywordsVIRAL PROTEIN / Influenza / NS1 / effector domain / W187A
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 / molecular replacement / Resolution: 1.9 Å
AuthorsKleinpeter, A.B. / Green, T.J. / Petit, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI116738 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI134693 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural analyses reveal the mechanism of inhibition of influenza virus NS1 by two antiviral compounds.
Authors: Kleinpeter, A.B. / Jureka, A.S. / Falahat, S.M. / Green, T.J. / Petit, C.M.
History
DepositionMay 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Non-structural protein 1
B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)26,9732
Polymers26,9732
Non-polymers00
Water3,747208
1
A: Non-structural protein 1

B: Non-structural protein 1


Theoretical massNumber of molelcules
Total (without water)26,9732
Polymers26,9732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y+1/2,-z-1/21
Buried area1380 Å2
ΔGint-6 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.785, 69.744, 104.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Non-structural protein 1 / NS1 / NS1A


Mass: 13486.564 Da / Num. of mol.: 2 / Fragment: effector domain / Mutation: W187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)
Strain: A/Brevig Mission/1/1918 H1N1 / Gene: NS / Plasmid: pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q99AU3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 298 K / Method: evaporation / Details: 30% PEG 3350, 0.2M di-Ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→29.67 Å / Num. obs: 19479 / % possible obs: 98.71 % / Redundancy: 7.1 % / Biso Wilson estimate: 24.85 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 54.9
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 8.99 / Num. unique obs: 1905 / CC1/2: 0.759 / Rpim(I) all: 0.099 / Rrim(I) all: 0.266 / % possible all: 98.45

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.67 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.5
RfactorNum. reflection% reflection
Rfree0.2123 1452 7.46 %
Rwork0.1697 --
obs0.173 19474 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.55 Å2 / Biso mean: 37.2713 Å2 / Biso min: 11.67 Å2
Refinement stepCycle: final / Resolution: 1.9→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 0 208 2094
Biso mean---42.29 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061914
X-RAY DIFFRACTIONf_angle_d0.7972586
X-RAY DIFFRACTIONf_chiral_restr0.056302
X-RAY DIFFRACTIONf_plane_restr0.004332
X-RAY DIFFRACTIONf_dihedral_angle_d11.8551174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.96790.29671430.21671761190498
1.9679-2.04670.25621420.21221777191998
2.0467-2.13980.26161420.18641762190499
2.1398-2.25260.22291420.18251764190699
2.2526-2.39370.23741440.17441787193199
2.3937-2.57840.2151460.18871798194499
2.5784-2.83770.21781440.18251790193499
2.8377-3.24790.23391470.17721830197799
3.2479-4.09020.19761480.15081854200299
4.0902-29.67390.17321540.14791899205397
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)
16.4681-0.1408-0.55329.2598-0.50167.2963-0.1026-0.14880.15150.20280.34690.10750.17080.0895-0.21110.14070.0325-0.00160.1767-0.01950.1714-0.2114-0.6735-13.8923
25.45940.4978-0.16944.6146-5.686.784-0.7532-1.6678-0.46311.45761.05370.3202-0.1674-0.35560.10980.5790.1028-0.00810.62470.12560.26450.1856-14.5746-0.5014
33.76183.7615-2.43576.6597-4.9714.9647-0.7448-1.6293-1.09940.0023-0.269-1.37681.14261.42610.80180.40880.18710.02650.53660.13890.454910.0246-17.2316-7.1078
43.82231.3726-0.52878.4232-2.10234.57370.1784-0.42520.0103-0.01070.05520.7910.6985-0.1365-0.13390.232-0.0066-0.01320.19570.02660.1725-1.2238-15.6752-12.88
52.86312.3768-0.36413.95460.57126.28260.0286-0.03090.0127-0.60910.3705-0.4412-0.6060.3111-0.20480.3079-0.00950.18180.29920.02830.36948.86440.0431-25.7526
62.7161-2.8905-0.38583.6873-2.04076.84120.2581-0.49530.38610.48580.3220.9693-0.0606-0.369-0.29510.1530.0228-0.00230.19220.02250.30960.2231-11.8097-9.977
75.5929-0.9884.67340.9626-0.19384.26430.0526-0.81770.91460.2448-0.3115-1.1318-0.05651.05460.35210.3874-0.13050.01190.650.02570.942217.7277-7.0487-11.5187
84.4655-1.77541.30345.9788-1.36815.2520.05750.1898-0.3495-0.50820.11750.08941.11420.1188-0.06040.44650.065-0.0020.1571-0.0430.2224.3721-19.7342-16.6832
97.3817-0.1189-4.58916.00883.97985.3784-0.09060.77570.4468-0.70310.19660.0881-0.1259-0.2005-0.18670.32310.020.01360.28670.0050.22824.2652-9.8987-26.9089
106.1441.4043-0.56297.5589-0.9687.2869-0.1108-0.0348-0.0933-0.32150.28890.1060.02-0.3755-0.11950.1563-0.05110.00080.14250.00190.16680.559-31.2457-38.6027
114.10322.2496-1.54484.4953-5.47816.9963-0.36260.39360.399-1.1353-0.19110.2510.3787-0.03940.45070.42340.0295-0.05720.47770.04180.35281.5682-17.9665-52.503
126.2047-3.59562.23495.41471.33882.97510.8471-0.31731.129-0.158-1.276-0.1723-1.04240.2511-0.72660.3617-0.2706-0.05830.94320.50310.483612.7059-13.2992-46.7683
137.8286-1.15652.50464.9239-3.02828.15730.1041.46620.85180.1517-0.6571-0.351-0.73530.57340.31460.2844-0.0823-0.00770.30210.10760.25724.8584-12.4063-45.5912
148.6687-4.41414.77162.8078-3.44626.5051-0.01420.2225-0.17470.43520.07480.4406-0.2656-0.1661-0.13660.0813-0.00510.03360.17530.00450.17120.9275-22.4775-36.0568
157.2779-1.85773.84646.0275-1.44132.08660.1813-0.05550.20670.78130.611-0.10551.16010.2916-0.16470.37270.0513-0.09880.31170.03340.27559.0838-31.812-26.3998
163.7392-0.02952.19986.5425-2.23545.98210.01620.24780.1145-0.40550.01140.28310.0275-0.09320.0530.1418-0.027-0.02410.17690.00380.16591.3254-20.3654-42.8406
171.16951.3351-1.99884.5229-5.42756.8018-0.48481.182-1.0771-0.6162-0.3453-1.47971.38992.74180.27290.42450.09550.15171.0023-0.08110.684818.4203-25.7894-39.658
183.6018-0.9072-0.88398.8843-3.60546.89540.0223-0.06630.5660.4856-0.01740.0168-0.83150.1733-0.02680.3009-0.04360.00310.133-0.03390.16525.1007-12.3165-36.1666
195.49441.86034.95378.25271.79314.5617-0.1121-0.4505-0.04311.13010.49810.59820.1563-0.2746-0.28180.2890.07230.01550.29660.00990.19414.5259-21.8783-25.8428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 86 through 99 )A86 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 106 )A100 - 106
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 120 )A107 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 136 )A121 - 136
5X-RAY DIFFRACTION5chain 'A' and (resid 137 through 143 )A137 - 143
6X-RAY DIFFRACTION6chain 'A' and (resid 144 through 162 )A144 - 162
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 170 )A163 - 170
8X-RAY DIFFRACTION8chain 'A' and (resid 171 through 195 )A171 - 195
9X-RAY DIFFRACTION9chain 'A' and (resid 196 through 205 )A196 - 205
10X-RAY DIFFRACTION10chain 'B' and (resid 86 through 99 )B86 - 99
11X-RAY DIFFRACTION11chain 'B' and (resid 100 through 106 )B100 - 106
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 112 )B107 - 112
13X-RAY DIFFRACTION13chain 'B' and (resid 113 through 126 )B113 - 126
14X-RAY DIFFRACTION14chain 'B' and (resid 127 through 136 )B127 - 136
15X-RAY DIFFRACTION15chain 'B' and (resid 137 through 143 )B137 - 143
16X-RAY DIFFRACTION16chain 'B' and (resid 144 through 162 )B144 - 162
17X-RAY DIFFRACTION17chain 'B' and (resid 163 through 170 )B163 - 170
18X-RAY DIFFRACTION18chain 'B' and (resid 171 through 195 )B171 - 195
19X-RAY DIFFRACTION19chain 'B' and (resid 196 through 205 )B196 - 205

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