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- PDB-8e21: The crystal structure of wild type PA endonuclease (2009/H1N1/CAL... -

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Basic information

Entry
Database: PDB / ID: 8.0E+21
TitleThe crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023034
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / 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-U9U / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsCuypers, M.G. / Slavish, J.P. / Rankovic, Z. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Citation
Journal: To Be Published
Title: The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023034
Authors: Cuypers, M.G. / Slavish, J.P. / Rankovic, Z. / 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
DepositionAug 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4426
Polymers23,1481
Non-polymers1,2935
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.523, 90.523, 134.983
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 Polymerase acidic protein


Mass: 23148.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1))
Strain: A/Luxembourg/43/2009(H1N1) / Gene: PA / Production host: Escherichia coli (E. coli) / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 11 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-U9U / 5-hydroxy-6-oxo-N-[2-(pyridin-4-yl)ethyl]-2-{[2-(trifluoromethyl)phenyl]methyl}-3,6-dihydropyrimidine-4-carboxamide


Mass: 418.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F3N4O3 / 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.: 6 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 10 MM MNCL2, 10 MM MGCL2, 0.5% PVP K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→75.18 Å / Num. obs: 8312 / % possible obs: 94.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 75.99 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 12.9
Reflection shellResolution: 2.61→2.73 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1058 / CC1/2: 0.841 / Rpim(I) all: 0.365 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VPT

5vpt


Resolution: 2.61→46.44 Å / SU ML: 0.3319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.9935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2764 390 4.7 %
Rwork0.2207 7912 -
obs0.2232 8302 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.51 Å2
Refinement stepCycle: LAST / Resolution: 2.61→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 78 6 1514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271542
X-RAY DIFFRACTIONf_angle_d0.63932083
X-RAY DIFFRACTIONf_chiral_restr0.0421218
X-RAY DIFFRACTIONf_plane_restr0.0045262
X-RAY DIFFRACTIONf_dihedral_angle_d8.3539225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.730.40661440.32722684X-RAY DIFFRACTION97.79
2.99-3.760.31991310.26762690X-RAY DIFFRACTION96.48
3.76-46.440.23561150.18742538X-RAY DIFFRACTION86.47
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)
15.133634758592.930519091384.86354859255.579913886811.188255319198.002811472850.8898053986221.626119563930.7277955447870.732000046071-0.6479217865750.400230761770.774817364186-0.170815544779-0.04410383915870.762768588864-0.1222577760340.2717939281770.734801640611-0.1072428778520.86615889419228.46944289623.62662587683.57110191639
26.9800648487-3.687056731871.433480755386.726344157041.872322866735.41507748926-0.02637585926550.13495474418-0.8948117434670.660712646509-0.4114598062050.02033093093581.63134479360.7017515051890.6434687384671.03110769375-0.05950870366540.3349680756230.730553212016-0.01102296486440.70421564266339.172165870617.58302903964.4498025134
33.945683265190.9659276842283.332365020593.440677898252.704357624176.53317921416-0.206931947418-0.0751433225593-0.07033231223941.13384852667-0.1876960840480.6014362592660.2428527988710.5933916616510.3280429114370.625192741334-0.1334430569250.3218770378050.5620919823070.002420029624610.77889023525736.219111370323.289099664714.3553323342
44.58065597363-2.59585110929-0.9046000702921.68491163449-0.3463769765954.258934429710.173110465298-0.3932275702630.570310010714-0.129292184703-0.00892947556046-1.05073090541-0.03347037141080.632933199959-0.223294283810.78460737243-0.08537132915320.232503871850.8975898192950.2229165988250.91003716710248.191509172928.41069379519.7772895488
57.415080136133.202503659545.53771206863.614346742823.665233273329.04947548095-0.306743444597-0.206509063243-0.912273354131.015586258130.055038761168-1.670015760760.4391158822832.095869065840.409937124990.9757211971140.2032591779730.1793284991070.9703816607780.3246365426490.72549364566556.5433636219.210328848319.0270540453
68.40398463355-3.405041740561.913486734043.925744158392.924049593455.820931343050.5075425047-1.02500855605-1.694202509062.191064906-0.09874285002020.659814423622-1.18281552656-1.03322543318-0.4013247061691.15869944315-0.1228998343350.2374513158280.9761591312420.4492503510210.88955673009450.586436342114.990959696823.455328731
71.99957301994-9.39672417551-4.300287845957.887239388743.611509634671.64946712812-1.26783049188-3.031183610430.1671698106780.7199312181670.088962134289-0.8882899311830.7853178871670.784950370954-0.01359230005470.900944321057-0.05447239037720.3095095810510.9869567718680.2513039474440.70209206355749.996225665426.672414881128.4441372667
86.52393278267-3.497367129422.141141975513.88500459488-1.86514422213.365691783410.517129821913-0.342715735941-2.085058989740.28672975926-0.615311057926-0.6159470442621.119814406730.05417594504730.1338978030010.797094457978-0.1705605656360.4615605757880.8397801892920.158272332730.86361796352437.220940660518.033355795823.7122320174
92.163552361043.442333407180.7147041802835.798011345180.8928737521135.460935221270.143052978267-0.02685067028090.3692345425351.399119827290.3527641140460.7633248529911.75863991274-0.328934000628-0.1336388024271.82258567517-0.05710500117730.195198241831.008005956290.2996983620530.82482794476635.110986989411.214147440627.4606126957
108.091820879672.621677925913.949177207584.757877153461.590011924397.581981191361.37093782275-1.7165242471-0.2598218309930.640651970048-0.869273929022-0.8603359064010.6144014294750.8402537578130.5292000552131.04079908513-0.2398848549860.5050621058370.861496151970.4690368486240.66828559387840.461372302617.39613985428.5412643479
113.69126982868-1.572242404263.779679763091.811273412090.4205123566077.4529453218-0.065609616223-0.970836541929-0.9552228932630.3133377842230.3023067247230.7219561966410.48104961774-0.28029597640.1401801959511.31191163498-0.1583252693810.3446034777110.9613184045670.1049115015650.7713885212534.148575152723.229368925130.4088617865
129.08574231337-1.89195731325.021507218982.961505230860.5748401145199.58994756989-0.6177871916910.636680003290.500822917393-0.125966618677-0.003105461789690.550678435667-0.430081126087-0.684661303060.5119429405320.666190394683-0.1862813718610.3600186974170.670572339259-0.06290946222030.76356632181726.745141422528.342522248719.188916932
139.13602091832-2.811084138917.212483341192.2968216748-1.507794258876.050160526661.07942830146-1.56895216259-1.104948530470.435860682516-0.4794021590671.238149395021.4123529204-2.043769386650.01127614335050.858709064159-0.4106928747220.3625844097020.907712209086-0.2168038815710.97879571100122.217287136616.133839735312.4602803592
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 - 102 - 14
22chain 'A' and (resid 11 through 31 )11 - 3115 - 35
33chain 'A' and (resid 32 through 50 )32 - 5036 - 54
44chain 'A' and (resid 51 through 83 )51 - 8355 - 68
55chain 'A' and (resid 84 through 98 )84 - 9869 - 83
66chain 'A' and (resid 99 through 108 )99 - 10884 - 93
77chain 'A' and (resid 109 through 115 )109 - 11594 - 100
88chain 'A' and (resid 116 through 126 )116 - 126101 - 111
99chain 'A' and (resid 127 through 138 )127 - 138112 - 123
1010chain 'A' and (resid 139 through 149 )139 - 149124 - 134
1111chain 'A' and (resid 150 through 164 )150 - 164135 - 149
1212chain 'A' and (resid 165 through 184 )165 - 184150 - 169
1313chain 'A' and (resid 185 through 195 )185 - 195170 - 180

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