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- PDB-7lp7: The crystal structure of the wild type PA endonuclease (2009/H1N1... -

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Basic information

Entry
Database: PDB / ID: 7lp7
TitleThe crystal structure of the wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000983476
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-YAD / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W.
Citation
Journal: To Be Published
Title: The crystal structure of the wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000983476
Authors: Cuypers, M.G. / Slavish, P.J. / 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
DepositionFeb 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 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

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4876
Polymers23,1481
Non-polymers1,3385
Water39622
1
A: Polymerase acidic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)195,89348
Polymers185,1878
Non-polymers10,70640
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area16990 Å2
ΔGint-239 kcal/mol
Surface area59890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.578, 89.578, 133.759
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 BL21(DE3) (bacteria) / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 27 molecules

#2: Chemical ChemComp-YAD / (phenylmethyl) (2~{S})-2-[5-oxidanyl-6-oxidanylidene-4-(2-pyridin-4-ylethylcarbamoyl)-1~{H}-pyrimidin-2-yl]pyrrolidine-1-carboxylate


Mass: 463.486 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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.: 22 / 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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop

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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: Apr 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→74.43 Å / Num. obs: 9782 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 57.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.087 / Net I/av σ(I): 1 / Net I/σ(I): 17
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.077 / Mean I/σ(I) obs: 2 / Num. unique obs: 1081 / CC1/2: 0.747 / Rpim(I) all: 0.442 / Rrim(I) all: 1.238 / Χ2: 0.96 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.5→44.79 Å / SU ML: 0.3365 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.3098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2566 480 4.91 %
Rwork0.2156 9293 -
obs0.2178 9773 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.82 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 75 22 1536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611548
X-RAY DIFFRACTIONf_angle_d0.86962093
X-RAY DIFFRACTIONf_chiral_restr0.0513219
X-RAY DIFFRACTIONf_plane_restr0.0068267
X-RAY DIFFRACTIONf_dihedral_angle_d20.1831565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.860.3721190.29893060X-RAY DIFFRACTION99.91
2.86-3.610.28731690.25493044X-RAY DIFFRACTION99.97
3.61-44.790.2321920.18693189X-RAY DIFFRACTION99.97
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)
11.33365445170.665880887895-1.204211116326.09944168494-2.400648646735.2341271886-0.3449166504720.461764678673-0.0926111285108-0.7175567923660.2428965751460.3268096343130.342270172314-0.7126612645540.1630188747420.5493847448380.0843947253777-0.04460240741610.767134332667-0.2473003801320.612526951269-23.49619854719.391512695967.98240003041
25.14355350817-1.20992443211-1.289156913487.55192307891.181906262314.40179167285-0.269590316828-0.483573907021-0.1626518918660.278511377599-0.1253704497280.5905501088080.132613503708-0.976214919080.3808518957370.506309528763-0.02578246286980.1632122912440.762606467183-0.1980634574960.496861637549-23.8592204131-3.5664498573622.0538912373
32.018009235278.018123828744.688932873357.338102927512.28324130515.383316588710.3776477370890.7993079755971.163250534891.52100238068-0.2846342600281.421494203511.20906753221-0.281562853695-0.2014050534360.8537576539930.1384896414880.1391436382241.72542091204-0.3879296919540.894308332158-34.11232288519.5995447978927.6748621783
40.5974787781380.291212121838-0.6305245408353.89950192123-1.02353184345.29308545642-0.209234377191-0.2277285435020.2670838529250.3412431365080.02621894415730.521387206711-0.542252920678-0.8729322769350.1618654913810.6426442086650.231419518628-0.0812747033670.817722606118-0.3281657239890.717182321382-22.490611454714.767983521922.2266548622
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 -1 through 51 )-1 - 513 - 55
22chain 'A' and (resid 52 through 126 )52 - 12656 - 111
33chain 'A' and (resid 127 through 138 )127 - 138112 - 123
44chain 'A' and (resid 139 through 195 )139 - 195124 - 180

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