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- PDB-7mty: The crystal structure of wild type PA endonuclease (2009/H1N1/CAL... -

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Basic information

Entry
Database: PDB / ID: 7mty
TitleThe crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988569
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN/Inhibitor / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / VIRAL PROTEIN-Inhibitor complex / Hydrolase / VIRAL PROTEIN
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / 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-W5V / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsCuypers, M.G. / Slavish, J.P. / Rankovic, Z. / White, S.W.
CitationJournal: 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
DepositionMay 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)24,5227
Polymers23,1481
Non-polymers1,3736
Water1448
1
A: Polymerase acidic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)196,17356
Polymers185,1878
Non-polymers10,98648
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area19240 Å2
ΔGint-369 kcal/mol
Surface area61800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.730, 89.730, 134.023
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 / RNA-directed RNA polymerase subunit P2


Mass: 23148.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 14 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-W5V / 2-(2,6-difluorophenyl)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide


Mass: 402.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16F2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 8 / 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: 2.91 Å3/Da / Density % sol: 57.78 %
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-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→74.56 Å / Num. obs: 11325 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 51.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.025 / Χ2: 1.05 / Net I/σ(I): 21.4
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.064 / Mean I/σ(I) obs: 2 / Num. unique obs: 1151 / CC1/2: 0.747 / Rpim(I) all: 0.461 / Χ2: 0.93 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7k87

7k87


Resolution: 2.38→38.44 Å / SU ML: 0.354 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.5446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2581 531 4.69 %
Rwork0.2198 10786 -
obs0.2217 11317 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.39 Å2
Refinement stepCycle: LAST / Resolution: 2.38→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 82 8 1533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211559
X-RAY DIFFRACTIONf_angle_d0.54662109
X-RAY DIFFRACTIONf_chiral_restr0.0398220
X-RAY DIFFRACTIONf_plane_restr0.0026266
X-RAY DIFFRACTIONf_dihedral_angle_d7.752226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.620.36251390.2862630X-RAY DIFFRACTION99.89
2.62-30.35341060.29462670X-RAY DIFFRACTION99.89
3-3.780.2861410.23932677X-RAY DIFFRACTION99.96
3.78-38.440.21831450.18832809X-RAY DIFFRACTION99.49
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)
14.00469582638-0.5154405681310.3611576711252.649452545971.149093322259.07626816007-0.2086253684360.487212354475-0.47759236105-0.232466216405-0.1244792152210.05203491383410.6444481285780.1774033356560.2572106700070.65352882371-0.1109739188060.2959498056870.426242446288-0.03613476242550.60623571069434.810145892720.48769025947.14654275824
24.74730479813-0.587708786525-0.05946546244982.72475598549-1.171491639544.093042767020.0672139568289-0.694969764183-0.6249018779290.746029033463-0.305300524731-0.05906362587840.599890894730.1684964053150.2872990843570.968618747496-0.01117374611940.2305299618480.6439708563990.2349673476060.54797676891846.183031488219.483501234223.05440214
34.95000819352-0.3778288583620.7821102320092.22708363092-0.3890028786334.31649060103-0.181805195599-0.585096210367-0.7090486659670.558746640767-0.09804423587660.4078804098980.525136289447-0.6344378662610.2165487799490.890605836298-0.2208088524410.4079672329460.6861418445230.006515688755810.68006643624830.027443431522.077721289222.1669197542
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 -4 through 50 )-4 - 501 - 55
22chain 'A' and (resid 51 through 137 )51 - 13756 - 123
33chain 'A' and (resid 138 through 195 )138 - 195124 - 181

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