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- PDB-7kop: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7kop
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease I38T mutant in complex with SJ000988539
ComponentsProtein PA-X
KeywordsVIRAL PROTEIN / Hydrolase / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE
Function / homology
Function and homology information


viral RNA genome replication / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA
Similarity search - Domain/homology
: / Hexa Vinylpyrrolidone K15 / Chem-WTM / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Seetharaman, J. / White, S.W.
Citation
Journal: To Be Published
Title: The crystal structure of the 2009/H1N1/California PA endonuclease I38T mutant in complex with SJ000988539
Authors: Cuypers, M.G. / Slavish, P.J. / Seetharaman, J. / White, S.W.
#1: Journal: Eur.J.Med.Chem. / Year: 2023
Title: Chemical scaffold recycling: Structure-guided conversion of an HIV integrase inhibitor into a potent influenza virus RNA-dependent RNA polymerase inhibitor designed to minimize resistance potential.
Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / ...Authors: Slavish, P.J. / Cuypers, M.G. / Rimmer, M.A. / Abdolvahabi, A. / Jeevan, T. / Kumar, G. / Jarusiewicz, J.A. / Vaithiyalingam, S. / Jones, J.C. / Bowling, J.J. / Price, J.E. / DuBois, R.M. / Min, J. / Webby, R.J. / Rankovic, Z. / White, S.W.
History
DepositionNov 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3956
Polymers23,1361
Non-polymers1,2595
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein PA-X
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)195,16448
Polymers185,0908
Non-polymers10,07340
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area21670 Å2
ΔGint-238 kcal/mol
Surface area60330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.594, 89.594, 131.826
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein PA-X


Mass: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus, (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1))
Gene: PA-X, PA / Strain: A/Luxembourg/43/2009(H1N1) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4D6EED0, UniProt: C6H0Y9

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Non-polymers , 5 types, 52 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-WTM / 2-(2-fluorophenyl)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-1,6-dihydropyrimidine-4-carboxamide


Mass: 384.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17FN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-QQ4 / Hexa Vinylpyrrolidone K15 / 1,1',1'',1''',1'''',1'''''-[(3R,5R,7R,9S,11R)-dodecane-1,3,5,7,9,11-hexayl]hexa(pyrrolidin-2-one)


Mass: 668.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56N6O6
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.86 Å3/Da / Density % sol: 56.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 0.1M MGCL2, 0.5% PVP K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→45.68 Å / Num. obs: 11600 / % possible obs: 98.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 48.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Net I/σ(I): 19.8
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1135 / CC1/2: 0.765 / Rpim(I) all: 0.468 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.33→45.68 Å / SU ML: 0.2554 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8857
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2283 598 5.16 %
Rwork0.2066 10999 -
obs0.2076 11597 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.59 Å2
Refinement stepCycle: LAST / Resolution: 2.33→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 76 47 1611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221599
X-RAY DIFFRACTIONf_angle_d0.56732158
X-RAY DIFFRACTIONf_chiral_restr0.0387225
X-RAY DIFFRACTIONf_plane_restr0.0027273
X-RAY DIFFRACTIONf_dihedral_angle_d13.2155230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.560.29281650.27472713X-RAY DIFFRACTION99.07
2.56-2.940.28011370.262728X-RAY DIFFRACTION98.76
2.94-3.70.25451450.21862743X-RAY DIFFRACTION98.13
3.7-45.680.19371510.17962815X-RAY DIFFRACTION95.71
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)
12.084915273870.327598204-0.5684351190537.649855235861.017970222282.211751130790.2197248110021.001376856170.324987997648-0.281336429046-0.192424672643-0.219256298694-0.6320056138230.1591063326970.02016058726510.688293695272-0.103940785627-0.1899236869980.608751394350.1088248512490.54456192303216.176376017421.21553998793.32321960614
29.2040689903-0.906097504888-1.800380012637.64853197889-0.8160414870296.572983723660.3805147427611.127047253620.850607498866-0.277295769695-0.4684484622090.142211864641-1.04083415285-1.045353898070.04147253816390.7445979679990.0797108516614-0.1998416632570.5777542006540.1061472619160.5597705606935.2634360673827.04733244884.14459282003
34.34997983803-1.03929725178-1.388200155711.37832733752-1.831003782954.73130272592-0.03435289919920.0781637438613-0.3787878247310.0804565932268-0.118925204254-0.05051519544710.0904820238016-0.6057096668280.1366799798510.478392346427-0.0713541434645-0.2006905420520.40779609841-0.1236039010390.4743955483513.7012661365619.750866805116.3747502272
43.13010128589-0.0631757667105-0.5741990949412.830157939350.8772533683042.55599691920.027789132326-0.7237153072890.5877060978860.499180899587-0.3392308499610.118482519036-0.589002220429-0.1581961081640.2518007586590.670371893003-0.0112715724526-0.1820287109620.54353597161-0.2375131840690.501460912587-3.8832313928625.636906256122.8165494248
56.51366480269-3.84568984215-0.5656845970035.989667934022.049156492983.216648533830.425707366421-0.5800245108890.424893945589-0.2781469093270.0714219649222-0.7579567394270.202758969743-0.0443712114386-0.4095063854961.55751587529-0.290946088564-0.1822065347190.798898668008-0.2033451883010.5851653085058.7500226457434.067324690426.9682751935
63.702843269720.7508918934960.2810478200923.47319285048-0.255615306073.651555540050.00297374190121-0.4858159152940.4577735670570.737819085139-0.222360244259-0.1484027512020.4670710374030.17090991599-0.0323600789380.66190275108-0.28131538526-0.2073947653890.541682553487-0.261539541420.4047465675794.3297567977627.875076993728.2770227206
74.96698789344-0.0514594167509-2.114779761511.767158052560.2593436883854.71467126621-0.0861035950634-0.8036352414850.04220449115770.29859294991-0.215744006160.0151275808818-0.2479808532160.853279800480.2286040663530.61520925265-0.147781636566-0.2930806893590.4649610002290.03348811050560.52838065801115.26460064319.054550419723.2183157931
82.85297905944.353306596122.457291161168.007805100914.036784846733.489891440530.14798327421-0.2546346183041.345132476-0.04509022622370.209096975169-0.966776549544-2.090196787621.32371947589-0.6013443243841.03196836699-0.309756333619-0.2170562916360.6637104166240.1029438129320.90970960093221.919087615830.52726408912.8875915676
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 10 )-2 - 107 - 19
22chain 'A' and (resid 11 through 31 )11 - 3120 - 40
33chain 'A' and (resid 32 through 83 )32 - 8341 - 73
44chain 'A' and (resid 84 through 126 )84 - 12674 - 116
55chain 'A' and (resid 127 through 138 )127 - 138117 - 128
66chain 'A' and (resid 139 through 149 )139 - 149129 - 139
77chain 'A' and (resid 150 through 185 )150 - 185140 - 175
88chain 'A' and (resid 186 through 195 )186 - 195176 - 185

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