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- PDB-8dip: The crystal structure of I38T mutant PA endonuclease (2009/H1N1/C... -

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Basic information

Entry
Database: PDB / ID: 8dip
TitleThe crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001023030
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-SE9 / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCuypers, M.G. / Slavish, J.P. / Rankovic, Z. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
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
DepositionJun 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4456
Polymers23,1361
Non-polymers1,3095
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.316, 89.316, 134.121
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: PA / Production host: Escherichia coli (E. coli) / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 30 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-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-SE9 / (2P)-5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[3-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide


Mass: 434.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F3N4O4 / Feature type: SUBJECT OF INVESTIGATION
#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.: 25 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
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 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→74.34 Å / Num. obs: 9604 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 61.011 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Χ2: 0.64 / Net I/av σ(I): 13.1 / Net I/σ(I): 13.1
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1081 / CC1/2: 0.845 / Rpim(I) all: 0.373 / Χ2: 0.65 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VPT

5vpt


Resolution: 2.5→39.98 Å / SU ML: 0.5228 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.1988
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2703 504 5.26 %
Rwork0.2276 9086 -
obs0.2299 9590 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 79 25 1537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271546
X-RAY DIFFRACTIONf_angle_d0.64222092
X-RAY DIFFRACTIONf_chiral_restr0.0389218
X-RAY DIFFRACTIONf_plane_restr0.0039265
X-RAY DIFFRACTIONf_dihedral_angle_d12.4365224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.39931160.3572248X-RAY DIFFRACTION99.41
2.75-3.150.38521180.30142246X-RAY DIFFRACTION98.83
3.15-3.970.29091450.24122243X-RAY DIFFRACTION98.47
3.97-39.980.22681250.19192349X-RAY DIFFRACTION96.72
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)
14.29856405004-0.669062491691-3.650028598033.123323784881.387891680224.342037648350.3087386058421.73160509767-0.616493547617-0.386155951307-0.5726342361970.187850723301-1.01154553628-0.1804034648070.1403406666210.959904002242-0.149832217962-0.241591277510.6356242803820.02130063348940.68794849632510.824163854322.78826564844.41328501367
20.9250028294591.12050790332-1.318074673528.488637964482.194958253266.36165980014-0.498788433813-0.385716225151.88681848579-0.1126412121190.2323287670420.598302789653-2.22713030463-0.1516684798710.2836798778681.51294367746-0.0062935935477-0.3694335864351.107866244130.07755814492481.114545133578.8176092212233.19708166733.41883264509
34.116021660030.279989234709-1.411394232861.854732456930.4510343976612.84716399229-0.180541547697-0.0597409315792-0.04648311017430.47362894429-0.1946017565450.0155378793147-0.493163201565-0.6931539829010.3866215273370.7566124975950.00765683576129-0.2052606961580.662075781189-0.1358699766430.699000478746-0.77833286064221.801571969117.2187484012
45.15481636908-2.80602078813-2.045063436593.435792340261.669836994062.5529056313-0.0908430108711-1.053959197720.3212076085950.910775146837-0.3180775228190.0608570136637-1.197046826261.40846246211-0.1154101746520.982293352406-0.0687361980743-0.1618869784710.759649838748-0.241167767170.730242435171-5.4157923471824.78544428525.8256398814
54.40215168502-1.68290826099-1.832891577092.27308335061.5369021214.61325529220.552589766562-0.8493832913040.688387215760.958551163352-0.206621852896-0.438493362136-1.181849013850.550544847133-0.3355486586691.4125856704-0.273537196922-0.3158854611390.794710570083-0.200974089190.8420349893139.2362658969230.409186968925.5527650768
65.56950344986-0.875756097495-1.331249146010.8409002710120.3703398095673.43939360757-0.0108482689119-0.5870001885770.2777848214110.399845023013-0.135359511509-0.359406134681-0.9870492938880.4196248754460.2268303294910.820473037132-0.211841526304-0.3196316657310.694078344839-0.04098791128780.7665870180515.029796880622.746382910522.323294195
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 23 )-1 - 233 - 27
22chain 'A' and (resid 24 through 31 )24 - 3128 - 35
33chain 'A' and (resid 32 through 98 )32 - 9836 - 83
44chain 'A' and (resid 99 through 115 )99 - 11584 - 100
55chain 'A' and (resid 116 through 137 )116 - 137101 - 122
66chain 'A' and (resid 138 through 195 )138 - 195123 - 180

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