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- PDB-7my5: The crystal structure of wild type PA endonuclease (2009/H1N1/CAL... -

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Basic information

Entry
Database: PDB / ID: 7my5
TitleThe crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988503
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / Hydrolase/Inhibitor / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / Hydrolase-Inhibitor complex
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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-Y5V / 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.
Citation
Journal: To Be Published
Title: The crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000988503
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
DepositionMay 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 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)24,6118
Polymers23,1481
Non-polymers1,4627
Water18010
1
A: Polymerase acidic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)196,88564
Polymers185,1878
Non-polymers11,69956
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
crystal symmetry operation5_455-x-1,y,-z1
crystal symmetry operation6_545x,-y-1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_445-y-1,-x-1,-z1
Buried area20440 Å2
ΔGint-425 kcal/mol
Surface area60660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.591, 89.591, 133.076
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, 17 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-Y5V / 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-2-(2-methylphenyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide


Mass: 395.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21N3O5 / 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.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
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→74.32 Å / Num. obs: 11227 / % possible obs: 100 % / Redundancy: 6.1 % / Biso Wilson estimate: 57 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Χ2: 0.99 / Net I/σ(I): 20.5
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.003 / Mean I/σ(I) obs: 2 / Num. unique obs: 1150 / CC1/2: 0.738 / Rpim(I) all: 0.443 / Χ2: 0.95 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LM4

7lm4


Resolution: 2.38→66.54 Å / SU ML: 0.3624 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0953
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.258 573 5.11 %
Rwork0.2131 10647 -
obs0.2152 11220 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.52 Å2
Refinement stepCycle: LAST / Resolution: 2.38→66.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 87 10 1539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211561
X-RAY DIFFRACTIONf_angle_d0.53322111
X-RAY DIFFRACTIONf_chiral_restr0.0384219
X-RAY DIFFRACTIONf_plane_restr0.0028266
X-RAY DIFFRACTIONf_dihedral_angle_d18.4951565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.620.35071730.28332560X-RAY DIFFRACTION99.85
2.62-30.35511200.28222639X-RAY DIFFRACTION99.93
3-3.780.30271410.22942648X-RAY DIFFRACTION100
3.78-66.540.20561390.18332800X-RAY DIFFRACTION99.9
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)
14.323106040871.64021393128-5.21445400554.030489748361.008634582539.26852110515-0.15766929787-0.4981125805160.1145326485452.049273537840.330141110180.5851522225790.3452021088940.864701378144-0.2692544069270.689263455655-0.0297262926723-0.03641408509220.7747361395310.1495468148830.670787250781-22.9154411137-28.2126708793-3.19642339971
22.81286069209-0.1825160536720.8025142104685.931228260173.622519188223.33882500654-0.315895958076-0.2671688743530.1018274725310.609220453310.138020597789-0.3701840819390.6374487992380.5550022476210.1111017574280.576803031517-0.02082273567760.004477558672060.7778999657860.2978237771540.676113893634-20.1149744222-37.6880555204-9.09130056623
32.67719310757-0.914915468044-0.7665063329188.21261145878-1.086035207874.58847195891-0.2773816215680.40940609475-0.278811508546-0.4763337278660.0781182806375-0.3357594379830.3595268934610.5948010553270.1534103655940.465706260154-0.03849363256250.2028853642120.6997461836970.1881520953650.541933510277-21.1960031958-48.4736429468-22.1170247614
47.27510359253-2.096050205990.4441587172488.132225120522.067016320385.832533829070.8065481584290.3001746597151.20357983831-0.9498325899820.139758386242-1.17362741879-0.8191646245850.573162269451-1.036388645860.79588095847-0.2584544932880.1758170674411.696188265560.1029279465040.812844291646-10.6057930276-35.5098650422-27.3392332974
52.87237318446-1.69806082763-0.8738568440076.611204540944.784353077093.91262749438-0.02709710954820.50163002460.162328428283-1.295904309480.00798575330754-0.603670038676-0.471344419997-0.352032338099-0.009569210809310.702595121039-0.1362421213930.1273019294060.8274286055360.2672159013720.643027301061-20.8805439042-36.7259875734-29.4256850626
63.993552596641.498708057063.554153896547.709843059897.246727958189.32433353755-0.0608497613371-0.4873652837420.293104188345-0.543666750535-0.4706048120220.127131673052-0.789721292549-0.3248397245570.2987438835340.53615122072-0.121263603917-0.05115114998250.6137439217770.2941039674430.610677922299-27.5679623047-26.2068527791-18.707749731
72.36530078982-1.29996981087-4.167215095252.556231736313.00920141448.129860316750.03646103658460.3133163418521.54837625703-0.9770142546990.444306587027-1.19126550117-1.731775258591.15405551101-0.2541521538310.78506310882-0.372965422073-0.1042444661911.042642614170.2612661794650.976424995943-14.2205573511-22.5070927508-13.1908031996
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 126 )51 - 12655 - 111
44chain 'A' and (resid 127 through 138 )127 - 138112 - 123
55chain 'A' and (resid 139 through 164 )139 - 164124 - 149
66chain 'A' and (resid 165 through 185 )165 - 185150 - 170
77chain 'A' and (resid 186 through 195 )186 - 195171 - 180

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