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- PDB-7k87: The crystal structure of the 2009 H1N1 PA endonuclease in complex... -

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Basic information

Entry
Database: PDB / ID: 7k87
TitleThe crystal structure of the 2009 H1N1 PA endonuclease in complex with SJ000986436
ComponentsProtein PA-X
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE
Function / homology
Function and homology information


viral translational frameshifting / 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-W5V / PA-X protein / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Jayaraman, S. / 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
DepositionSep 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: 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

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Assembly

Deposited unit
A: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3175
Polymers23,1361
Non-polymers1,1814
Water77543
1
A: Protein PA-X
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)194,53940
Polymers185,0908
Non-polymers9,44932
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 area17960 Å2
ΔGint-140 kcal/mol
Surface area58880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.502, 89.502, 132.791
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

#1: Protein Protein PA-X


Mass: 23136.289 Da / Num. of mol.: 1
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 BL21(DE3) (bacteria) / References: UniProt: A0A4D6EED0, UniProt: C6H0Y9
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
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: 2.87 Å3/Da / Density % sol: 57.2 %
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: 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: 2.7→45.81 Å / Num. obs: 7507 / % possible obs: 98 % / Redundancy: 5.6 % / Biso Wilson estimate: 57.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.042 / Rrim(I) all: 0.101 / Χ2: 1.01 / Net I/σ(I): 17.7
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.995 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5615 / CC1/2: 0.649 / Rpim(I) all: 0.453 / Rrim(I) all: 1.097 / Χ2: 0.98 / % possible all: 98.8

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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: 2.7→44.75 Å / SU ML: 0.4479 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1941
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 377 5.02 %
Rwork0.2054 7127 -
obs0.207 7504 97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.45 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 72 43 1560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231565
X-RAY DIFFRACTIONf_angle_d0.57532116
X-RAY DIFFRACTIONf_chiral_restr0.0409221
X-RAY DIFFRACTIONf_plane_restr0.0035268
X-RAY DIFFRACTIONf_dihedral_angle_d9.0119226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.090.38651490.29252317X-RAY DIFFRACTION98.13
3.09-3.890.24151080.20982373X-RAY DIFFRACTION97.56
3.89-44.750.1921200.18052437X-RAY DIFFRACTION95.41
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)
15.72037152247-1.767253868831.509461126043.073476170650.1669157624655.870350417770.1724822824960.881567572719-0.416319714981-0.576419470526-0.401004388790.05091560133860.7724890195550.4064808205990.140052332210.749765503508-0.0223160104880.2341193927790.65168059741-0.03039212743950.53223436425135.202902778720.83416215957.59404373687
27.06423015616-0.490270807715-0.5169199035682.55730705479-1.153640926412.721545736530.0608814305784-0.389303029389-0.1508286766160.421688734918-0.283848483702-0.2912665767210.5158138849860.2302574031380.175018083070.804739596888-0.04005955599830.1516736076480.6068866522320.2153317523930.47006604321748.446969966121.276015945822.0889174294
30.576946318123-0.2312803769410.09080267446760.1209842657140.003668992167560.07116554580450.0842861417765-0.0523414838376-0.199489061644-0.4723210158230.398644046690.4149084680180.490167687648-0.4087381620450.213482098021.40070271546-0.05101647482590.1948939441820.5996617060870.2727439441880.69984423853835.09774824810.929102853527.6447007861
44.22559245809-0.1322858343671.742563240490.749254370698-0.778300983835.607147092080.0413095247223-0.477760856284-0.1921135833370.192199359058-0.1574096959290.2072909981690.567831532272-0.58398818656-0.01665741791740.789363460269-0.1770468317780.3172959958410.535738729133-0.006984191877660.5328037306229.932419026822.266263553222.1064719076
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 50 )-2 - 503 - 55
22chain 'A' and (resid 51 through 126 )51 - 12656 - 112
33chain 'A' and (resid 127 through 138 )127 - 138113 - 124
44chain 'A' and (resid 139 through 195 )139 - 195125 - 181

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