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- PDB-7knr: The crystal structure of the I38T mutant PA endonuclease (2009/H1... -

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Basic information

Entry
Database: PDB / ID: 7knr
TitleThe crystal structure of the I38T mutant PA endonuclease (2009/H1N1/California) in complex with SJ000988558
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-WTD / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Jayaraman, S. / White, S.W.
Citation
Journal: To Be Published
Title: The crystal structure of the I38T mutant PA endonuclease (2009/H1N1/California) in complex with SJ000988558
Authors: Cuypers, M.G. / Slavish, P.J. / Jayaraman, S. / 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
DepositionNov 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: 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)24,6218
Polymers23,1361
Non-polymers1,4847
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein PA-X
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)196,96564
Polymers185,0908
Non-polymers11,87456
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 area21270 Å2
ΔGint-444 kcal/mol
Surface area57490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.173, 89.173, 131.846
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 Protein PA-X


Mass: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T
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

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Non-polymers , 5 types, 38 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-WTD / 2-(2,6-difluorophenyl)-5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-3,6-dihydropyrimidine-4-carboxamide


Mass: 417.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F2N3O5 / 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.: 31 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
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: 2.48→45.57 Å / Num. obs: 9573 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 46.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Net I/σ(I): 18.1
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1065 / CC1/2: 0.689 / Rpim(I) all: 0.446 / % possible all: 99.4

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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: 2.48→39.42 Å / SU ML: 0.3658 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 468 4.89 %
Rwork0.2051 9104 -
obs0.2074 9572 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.17 Å2
Refinement stepCycle: LAST / Resolution: 2.48→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 88 31 1555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461556
X-RAY DIFFRACTIONf_angle_d0.70172104
X-RAY DIFFRACTIONf_chiral_restr0.0471218
X-RAY DIFFRACTIONf_plane_restr0.0048264
X-RAY DIFFRACTIONf_dihedral_angle_d6.8686223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.840.39021170.28663039X-RAY DIFFRACTION99.09
2.84-3.580.25461650.23352998X-RAY DIFFRACTION98.26
3.58-39.420.22521860.17653067X-RAY DIFFRACTION96.39
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)
13.73247151036-1.04569746075-1.64217859795.9470487423-3.130253768168.51646847363-0.170855402758-0.1683154441880.297245930885-1.46322277050.405918458007-0.167847012505-0.1601687745-1.19403144829-0.3853656288370.7221046259530.0367232578136-0.1250432902890.697779501894-0.1765168218280.494679901527-21.187233681316.16309797743.32939893728
26.756254326490.4458449986561.218656977728.67040299128-2.940326150296.644277593740.183758871150.988591513166-0.417563127264-0.8772869214770.1418011701040.9503812828110.86995845969-0.989194176591-0.2904790573380.536543932467-0.0800361653602-0.02192856049290.741943790363-0.2279965909730.581921718571-26.91823464135.369487225464.10891728933
30.8551618109770.6674094142690.7436464879174.26788327664-1.286852314774.85435372411-0.2249129875710.114597497772-0.01797529836350.0310284441265-0.0386461441567-0.1352029619220.471730200030.1626049370660.2399724143220.4128800914890.07391407731090.07368351078010.527449027098-0.1944049231790.50778620985-19.73460052043.6425949628216.3341032202
42.89814135328-0.00831679415983-0.6012201384434.65762511604-0.9048807553893.13084372573-0.236382044752-0.4566230512770.01616033055230.548106721095-0.06590099678940.3807875301480.0911847611065-0.4149289283080.1759255301070.443363328534-0.01860264022070.1865481964720.585968303383-0.1229351583210.486112819616-25.5828061665-3.9109298273322.8264074468
55.117524461385.617672207283.008678635329.327974607010.7112069508783.870241971720.172368681856-0.06513144710710.9158658540971.193341192020.2351390645011.54987678159-0.449268772695-0.258625773611-0.505273061510.6360304371020.1622586910730.1779651359051.53249634102-0.2348204689540.719482523818-33.89672985568.8066422264226.9659050277
63.161669752990.309206663713-0.4639227675587.37011244734-4.35892882457.6406802882-0.153999682602-0.6504271923520.2371864564731.20810723651-0.06360309279930.295669906813-0.1119521482410.4685343112270.2448680691150.5291106808720.1559475691920.1167370747360.665071820213-0.2270607148250.493836780814-23.86048819948.0631465939829.2602395346
70.8944812189111.15960001912-0.2542729971871.61915585315-1.06903278413.24576054575-0.1981972662040.1882579690470.463310376842-0.0240576007328-0.122572648006-0.131247559668-0.553973347171-0.481613269270.1941921529320.4736135906120.19313115475-0.1325735898330.587780693812-0.3041261366620.603692283911-21.353558430719.419374839916.7154967226
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 10 )-2 - 101 - 13
22chain 'A' and (resid 11 through 31 )11 - 3114 - 34
33chain 'A' and (resid 32 through 83 )32 - 8335 - 67
44chain 'A' and (resid 84 through 126 )84 - 12668 - 110
55chain 'A' and (resid 127 through 138 )127 - 138111 - 122
66chain 'A' and (resid 139 through 164 )139 - 164123 - 148
77chain 'A' and (resid 165 through 195 )165 - 195149 - 179

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