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

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Basic information

Entry
Database: PDB / ID: 8dvo
TitleThe crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023044
ComponentsProtein PA-X
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-U0I / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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 SJ001023044
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
DepositionJul 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 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: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5837
Polymers23,1481
Non-polymers1,4346
Water64936
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.067, 90.067, 134.090
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
Components on special symmetry positions
IDModelComponents
11A-336-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein PA-X


Mass: 23148.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / 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, 42 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-U0I / 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-2-{[2-(trifluoromethyl)phenyl]methyl}-1,6-dihydropyrimidine-4-carboxamide


Mass: 463.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20F3N3O5 / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.94 Å3/Da / Density % sol: 58.12 %
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: 2.33→74.77 Å / Num. obs: 12070 / % possible obs: 99.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 72.2 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.024 / Net I/σ(I): 14.2
Reflection shellResolution: 2.33→2.41 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1182 / CC1/2: 0.798 / Rpim(I) all: 0.393

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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: 2.33→63.69 Å / SU ML: 0.3574 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.7006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2724 624 5.18 %
Rwork0.2236 11430 -
obs0.226 12054 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.95 Å2
Refinement stepCycle: LAST / Resolution: 2.33→63.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 86 36 1568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311565
X-RAY DIFFRACTIONf_angle_d0.72652115
X-RAY DIFFRACTIONf_chiral_restr0.0447219
X-RAY DIFFRACTIONf_plane_restr0.0041266
X-RAY DIFFRACTIONf_dihedral_angle_d7.7541226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.560.33831800.29682811X-RAY DIFFRACTION99.67
2.56-2.940.33711460.3072806X-RAY DIFFRACTION99.23
2.94-3.70.33531470.26912872X-RAY DIFFRACTION99.64
3.7-63.690.23561510.18942941X-RAY DIFFRACTION97.29
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)
13.828758270541.303012461211.269129377068.60748614144-2.653022765134.99699048308-0.0575634690435-1.726370206670.9804969074161.409385552380.351060626030.432150954610.481077925014-0.135354283903-0.3164764524670.73401261123-0.1868466127780.08879105190670.970045316803-0.2721638754310.77545762402722.911600282628.260732331-3.15002886188
21.237547899980.3068397336950.760296189623.01661011731-1.613180862034.86285993621-0.0988547599139-0.1812517020860.007441807717670.497529217589-0.185895594950.0559869816308-0.701013726298-0.2481978199710.3305675499690.558541720914-0.0476417280141-0.003703968281650.767679185193-0.2868619714650.81377344848220.070693875537.6097127027-9.20442086676
31.75095560385-1.825770731760.1681365233664.99819499317-0.6039933317512.66958746021-0.2417686568950.6892844156050.64577989615-0.374438910509-0.135686999424-0.0901183243458-0.595404636017-0.4233849327260.3592641609010.691203033804-0.00935536579818-0.2409468303650.998062889232-0.1793290069240.75916900760622.375242973651.6226014636-21.7356603246
41.47274370495-0.5930133006071.046198558082.43723628589-0.02904090534512.42184327843-0.5287637377990.43988238758-0.466485866834-1.037780461950.6031886821320.666847055390.156352132389-0.888371835084-0.1123181375220.935883812181-0.155844338029-0.230555509111.34583129938-0.2826088727270.93381242409114.170237649836.5329294772-25.615484929
54.487833876141.84898919539-1.400770988657.0389264702-2.871732625194.25781940688-0.08772734407910.87846588682-0.237225704247-0.2241005014470.09384637379751.52573977384-0.708347136244-0.7844451965480.0241643702841.02301621191-0.0812725549322-0.2428622041221.06025051595-0.4548237305670.88452476208517.090503020740.3620188609-28.2956577953
61.47261232242-2.00846140605-0.6048404245319.41340380014-1.861301820284.643647272560.2446315697430.0417351689928-0.314047759872-2.01741752383-0.1306794464641.022589875540.290850999567-0.2721714765410.1552480714280.855591496247-0.228529686037-0.1358085975061.40239047713-0.3404773983960.80311875156623.474946099233.986814938-30.1936895752
73.851737363952.32164151431-2.559129514077.24540188153-4.322575328656.627954503590.02266744131570.040290044131-0.8807536164160.305022783149-0.824084953508-0.5914882124090.168365852880.4780138835390.7517194570260.717636524312-0.1441674164860.0778097529520.674367788015-0.2935461916140.72616832833927.83468700126.3397180408-18.811485148
80.864278143662-1.927978301060.451195467094.47964759051-2.038979403925.07238241170.09247929084260.865970071225-1.41692982098-0.6944388319310.2821489751952.080682144611.44386650879-1.65535032283-0.1310732426930.962103621601-0.4549523434710.0956553958561.00440808339-0.3350911496921.229700234714.419101633522.1958759416-13.1862737234
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 -3 through 10 )-3 - 101 - 14
22chain 'A' and (resid 11 through 50 )11 - 5015 - 54
33chain 'A' and (resid 51 through 115 )51 - 11555 - 100
44chain 'A' and (resid 116 through 138 )116 - 138101 - 123
55chain 'A' and (resid 139 through 149 )139 - 149124 - 134
66chain 'A' and (resid 150 through 164 )150 - 164135 - 149
77chain 'A' and (resid 165 through 185 )165 - 185150 - 170
88chain 'A' and (resid 186 through 195 )186 - 195171 - 180

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