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- PDB-7lw6: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7lw6
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease I38T mutant in complex with Raltegravir
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / Hydrolase / 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-RLT / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsCuypers, M.G. / Slavish, P.J. / White, S.W. / Rankovik, Z.
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
DepositionFeb 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)24,4566
Polymers23,1361
Non-polymers1,3195
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Polymerase acidic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)195,64448
Polymers185,0908
Non-polymers10,55440
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 area17970 Å2
ΔGint-238 kcal/mol
Surface area61710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.515, 89.515, 133.802
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: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T
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: Influenza A virus / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 24 molecules

#2: Chemical ChemComp-RLT / N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-di hydropyrimidine-4-carboxamide / RALTEGRAVIR, MK0518


Mass: 444.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21FN6O5 / 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.: 19 / 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: 57.53 %
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-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→74.4 Å / Num. obs: 11154 / % possible obs: 99.3 % / Redundancy: 5.7 % / Biso Wilson estimate: 74.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.024 / Rrim(I) all: 0.057 / Χ2: 1.02 / Net I/σ(I): 15.1
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1144 / CC1/2: 0.786 / Rpim(I) all: 0.455 / Rrim(I) all: 1.147 / Χ2: 1.08 / % possible all: 98.8

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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: 2.38→38.35 Å / SU ML: 0.2567 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6062
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2646 524 4.7 %
Rwork0.2164 10616 -
obs0.2188 11140 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.5 Å2
Refinement stepCycle: LAST / Resolution: 2.38→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 72 19 1524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121539
X-RAY DIFFRACTIONf_angle_d0.87282084
X-RAY DIFFRACTIONf_chiral_restr0.0397218
X-RAY DIFFRACTIONf_plane_restr0.0029264
X-RAY DIFFRACTIONf_dihedral_angle_d18.5603558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.620.29521380.24792595X-RAY DIFFRACTION98.88
2.62-30.3541040.28722654X-RAY DIFFRACTION99.6
3-3.780.28261400.24342643X-RAY DIFFRACTION99.36
3.78-38.350.24481420.19172724X-RAY DIFFRACTION97.15
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)
19.577740949661.477819923260.7580589989385.820853890313.315480599732.324993261120.4030496978660.913618299907-0.6046695217290.518398534099-0.329220994786-0.08421575430571.191811082850.21694460965-0.09352612811181.009545606430.01018048683040.2032293020590.776118682108-0.0003644252252110.53703905030434.105059290319.16128355093.60167543943
25.45183764781-0.08231308077912.291077308682.79384562849-0.1607252645421.947418056730.106615659833-0.03469702075890.07674146005740.340404133049-0.167206826438-0.1034300095050.5559482344140.09612844290570.05682541526210.7277760985070.02615318597460.1885274798770.6053579972430.1266594286940.53512237013346.947295448822.355680167819.5947767413
36.578017638050.6915484168882.901448328164.680004832330.03520229274323.998255798990.276460261271-1.49341269879-0.761994837501-0.147001109241-0.1647627738580.4072979661220.56399463316-0.713308413201-0.1110502712390.912219762746-0.1451151451980.2338417295320.6105900299080.2186957557120.66401714300136.874250757417.706124633624.0347399502
44.20788184843-0.6298440684132.238677803220.970263495934-0.1239126369716.23537342460.086809267155-0.538152478526-0.1569579639950.295215526179-0.2308701854640.02717574274370.823233693413-0.5262382750670.04621414010140.851917526846-0.2604269244210.2524567539520.6408378756710.0253160229360.59201166429830.981422229920.096841478923.2696509068
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 31 )-4 - 311 - 36
22chain 'A' and (resid 32 through 115 )32 - 11537 - 101
33chain 'A' and (resid 116 through 126 )116 - 126102 - 112
44chain 'A' and (resid 127 through 194 )127 - 194113 - 180

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