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

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Basic information

Entry
Database: PDB / ID: 8edz
TitleThe crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ000986319
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-WFW / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCuypers, M.G. / Slavish, J.P. / Jayaraman, S. / Rankovic, Z. / White, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Citation
Journal: To Be Published
Title: The crystal structure of I38T mutant PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ000986319
Authors: Cuypers, M.G. / Slavish, J.P. / 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
DepositionSep 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / 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)24,5186
Polymers23,1361
Non-polymers1,3815
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.688, 89.688, 132.251
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: Escherichia coli (E. coli) / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 25 molecules

#2: Chemical ChemComp-WFW / benzyl [2-(6-{[2-(4-amino-7H-pyrrolo[2,3-d]pyrimidin-7-yl)ethyl]carbamoyl}-5-hydroxy-4-oxo-1,4-dihydropyrimidin-2-yl)propan-2-yl]carbamate


Mass: 506.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26N8O5 / 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.: 20 / 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: 2.87 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: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→74.23 Å / Num. obs: 7865 / % possible obs: 97.4 % / Redundancy: 6 % / Biso Wilson estimate: 75.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.022 / Net I/σ(I): 17
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1032 / CC1/2: 0.798 / Rpim(I) all: 0.355 / % possible all: 98.5

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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: 2.65→31.71 Å / SU ML: 0.3803 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.8967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2716 390 4.96 %
Rwork0.2117 7469 -
obs0.2147 7859 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.53 Å2
Refinement stepCycle: LAST / Resolution: 2.65→31.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 75 20 1508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251522
X-RAY DIFFRACTIONf_angle_d0.65622064
X-RAY DIFFRACTIONf_chiral_restr0.0424218
X-RAY DIFFRACTIONf_plane_restr0.0029261
X-RAY DIFFRACTIONf_dihedral_angle_d7.0729222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-3.030.40681150.3052463X-RAY DIFFRACTION97.47
3.03-3.820.29771610.22892453X-RAY DIFFRACTION96.99
3.82-31.710.23131140.18982553X-RAY DIFFRACTION94.44
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)
16.732842706220.349988889630.2800769094362.689708411851.955847777178.14153055414-0.341809426338-0.8889506212320.08538406160881.362768936890.3138354713050.3821051585810.208808019680.9066165230010.02692746961480.7486307640810.0510227221902-0.06502624313350.8884597395350.1796980533830.600197334919-20.1949012843-35.109493621-3.97951284806
22.78811479255-0.8163257093830.3132200818537.406479674553.517722587771.83934877082-0.154692651330.0998709905790.234877233510.575590893866-0.1625064740370.5616217261670.7118954978850.1830728541820.4844840472860.608002571302-0.07637961603260.0864721109570.6307873324280.1742522594760.635366814264-25.0033604219-41.2217259883-16.3318852945
34.185899576630.7935320831810.4206346074466.211176129992.222703282492.58477341038-0.2839746494460.630707964365-0.174062554367-0.2787640166160.257132033375-0.1887964607140.3168000437150.7573774598430.1030906702890.634030085534-0.0007585367996770.1800028275540.7905504053370.16489826790.57897561935-19.1327799564-48.9130275929-22.9357649899
43.24789093447-2.249413750054.175655502552.06751879388-2.724476937525.880085231360.400379756268-2.77248943150.375951381836-0.318237173974-0.0715120223319-0.492525877361.13816220402-1.54607749283-0.7370104262370.948383017387-0.2098142905790.09791159270041.648917247540.01324648557240.820168599287-10.6362167081-36.0496977246-26.964924496
55.826607602290.4540159847641.575249917126.333493869543.487688490344.60731898463-0.255789084620.4476383574420.342125389135-0.6452424403720.0737667967122-0.01827221300370.0338027762269-0.6230307731360.07476460292710.677401523559-0.214454668840.05957262720530.7892752150030.2077982864630.558146949717-20.4687979382-36.8439053023-29.3123708945
62.3279647099-1.962594996431.823120300957.02187470764.611985648379.45393508569-0.156902887747-0.632167689806-0.3125149949790.1928227644660.128749957875-0.292044445912-0.2515439676840.2570004584370.02699647305760.509494824529-0.225417336881-0.01370430390940.6200022905550.2779213628710.697404425838-23.0748412332-25.2522612041-16.5416708599
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 31 )-1 - 311 - 33
22chain 'A' and (resid 32 through 83 )32 - 8334 - 66
33chain 'A' and (resid 84 through 126 )84 - 12667 - 109
44chain 'A' and (resid 127 through 138 )127 - 138110 - 121
55chain 'A' and (resid 139 through 164 )139 - 164122 - 147
66chain 'A' and (resid 165 through 195 )165 - 195148 - 178

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