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

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Basic information

Entry
Database: PDB / ID: 7uuh
TitleThe crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with compound SJ001034732-2 (cis-form)
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
: / Chem-NVR / Hexa Vinylpyrrolidone K15 / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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
DepositionApr 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
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
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)24,5397
Polymers23,1481
Non-polymers1,3906
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.980, 90.980, 134.738
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 (E. coli) / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 25 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-NVR / (1P,18Z)-5-hydroxy-16,21-dioxa-3,8,28-triazatetracyclo[20.3.1.1~2,6~.1~11,15~]octacosa-1(26),2(28),5,11(27),12,14,18,22,24-nonaene-4,7-dione / SJ001034732-1 (Cis-form)


Mass: 419.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N3O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
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-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→75.4 Å / Num. obs: 6568 / % possible obs: 99.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 83.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.032 / Χ2: 1.07 / Net I/σ(I): 18.6
Reflection shellResolution: 2.89→3.07 Å / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2 / Num. unique obs: 1045 / CC1/2: 0.789 / Rpim(I) all: 0.418 / Χ2: 0.94 / % possible all: 99.3

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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: 2.89→38.95 Å / SU ML: 0.3567 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2831 307 4.73 %
Rwork0.2495 6189 -
obs0.2511 6496 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.38 Å2
Refinement stepCycle: LAST / Resolution: 2.89→38.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 84 19 1514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341530
X-RAY DIFFRACTIONf_angle_d0.66462072
X-RAY DIFFRACTIONf_chiral_restr0.0447218
X-RAY DIFFRACTIONf_plane_restr0.0037262
X-RAY DIFFRACTIONf_dihedral_angle_d20.1093544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.640.37081660.3083034X-RAY DIFFRACTION98.25
3.64-38.950.25341410.23223155X-RAY DIFFRACTION96.91
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)
17.136217616650.1425601269985.324625990312.25496458905-0.5717353262874.17320837762-0.71686597419-0.593592765633-1.23717979846-0.9367902074840.354270657701-0.3920480092530.4286781508760.8454581387380.4835006745440.6122575281080.1003889944360.227682450180.6778678142520.2880530487091.0080346298823.0479959367-16.67437561652.30659222987
21.517615966362.029967936260.1079042053933.076587214620.3760811781635.81112744921-0.378927560789-0.612332566736-0.05090328494010.0273568654777-0.546468641544-0.468272858961-0.5216024098251.036090843740.873212976140.6279827029620.0860269495107-0.1726997952340.7930640621620.3324201662190.71751847610223.7464502491-1.4293410437313.2339451404
36.56496767350.211010078292-1.600991623215.189875112192.104808547449.32024389094-0.297209226709-1.23307613150.6805711245070.7880754860230.0872708667625-0.926594894048-0.008529998574720.5519437070820.1532418649130.7567928656890.134961129585-0.3987824726031.043869084980.1434024350230.83245628471524.68402845645.1235384152525.8807477051
41.53171524686-0.40125139875-0.3271113671182.483604267560.9328167888183.13443011855-0.242216104306-0.367506367943-0.128102546510.4364779416860.179513967649-0.3726977095580.5880198433970.191088047538-0.327874894790.9165933044540.281931559783-0.5381461174911.017144219980.5672656275930.92322984460426.9896948976-7.2317306141224.1226763958
51.986874658260.1562298131880.1679100241190.01882957944140.08872872301710.8430019264560.1460109702930.665126343409-0.04007956222610.0832066071636-0.257084929306-0.5549115132390.08247513488930.7219276881630.06242259777810.9430309298570.678906505331-0.1566733295362.421386955450.538471174150.88516152711134.021026926-10.490082094927.591610856
63.044169251290.8122601183473.19546544673.532970853492.056273218658.44254351273-0.187677189708-0.709912520451-0.3427502690540.976165786194-0.334389036153-0.6004847418490.6065338580520.3222561992220.1170672655330.7865272376890.179588127187-0.08162184483261.008453632230.4943391886830.78337799796120.8707456419-12.790536785125.1356569838
70.4634160620350.4023917677360.226539969212.331796850120.4231310247990.13614976095-0.472278885844-0.421928173532-0.1451168212240.8808864263750.36591360147-0.9827131074140.3022082100480.2438048251-0.04577880880691.04471887730.7395360481210.434113410140.9153569088310.5679384729131.4684146830128.973573929-23.410465124212.1091039185
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 10 )-4 - 101 - 15
22chain 'A' and (resid 11 through 98 )11 - 9816 - 84
33chain 'A' and (resid 99 through 115 )99 - 11585 - 101
44chain 'A' and (resid 116 through 126 )116 - 126102 - 112
55chain 'A' and (resid 127 through 137 )127 - 137113 - 123
66chain 'A' and (resid 138 through 184 )138 - 184124 - 170
77chain 'A' and (resid 185 through 195 )185 - 195171 - 181

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