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- PDB-6vbr: The crystal structure of the 2009 H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 6vbr
TitleThe crystal structure of the 2009 H1N1/California PA endonuclease wild type in complex with SJ000986248
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN/Inhibitor / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / HYDROLASE / VIRAL PROTEIN / VIRAL PROTEIN-Inhibitor complex
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-QVV / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsCuypers, M.G. / Slavish, P.J. / Rankovic, Z. / White, S.W.
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
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Structure summary / Category: citation / database_2 / struct
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Mar 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 1.3Oct 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)24,5316
Polymers23,1481
Non-polymers1,3825
Water37821
1
A: Polymerase acidic protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)196,24548
Polymers185,1878
Non-polymers11,05840
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 area19590 Å2
ΔGint-230 kcal/mol
Surface area61800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.790, 90.790, 134.118
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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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 BL21(DE3) (bacteria) / References: UniProt: C6H0Y9

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Non-polymers , 5 types, 26 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-QVV / benzyl [2-(4-{[2-(6-amino-9H-purin-9-yl)ethyl]carbamoyl}-5-hydroxy-6-oxo-1,6-dihydropyrimidin-2-yl)propan-2-yl]carbamate / SJ000988248


Mass: 507.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H25N9O5 / 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.: 21 / 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: 3.27 Å3/Da / Density % sol: 62.43 %
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, PH 6.5

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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: Aug 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→75.18 Å / Num. obs: 7619 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 89.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.022 / Rrim(I) all: 0.064 / Χ2: 1 / Net I/σ(I): 18.6
Reflection shellResolution: 2.75→2.88 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.173 / Mean I/σ(I) obs: 2 / Num. unique obs: 983 / CC1/2: 0.746 / Rpim(I) all: 0.404 / Rrim(I) all: 1.242 / Χ2: 0.97 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
PHENIXdev_3965refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.75→38.86 Å / SU ML: 0.591 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.0774
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2548 705 5.06 %
Rwork0.2389 13226 -
obs0.2397 7611 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.39 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 65 21 1491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611501
X-RAY DIFFRACTIONf_angle_d0.97812032
X-RAY DIFFRACTIONf_chiral_restr0.0592214
X-RAY DIFFRACTIONf_plane_restr0.0083257
X-RAY DIFFRACTIONf_dihedral_angle_d19.1969538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.960.41451680.39222606X-RAY DIFFRACTION99.93
2.96-3.260.38581470.33342645X-RAY DIFFRACTION99.96
3.26-3.730.30751290.29952645X-RAY DIFFRACTION99.89
3.73-4.70.22721440.22412648X-RAY DIFFRACTION99.82
4.7-38.860.21291170.19672682X-RAY DIFFRACTION99.75
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)
12.07552919657-2.01981398092-0.9731314155363.20423621332-1.699782912455.14284737823-0.3487042905730.232600169567-0.4876709439270.257809551375-0.003989400617980.582431022894-0.466824317472-0.8347721282360.3629088780210.792908373528-0.1303807060590.01262555307590.946634523774-0.3782489890461.1305818930521.330509534435.7810006549-7.70624814372
22.29813432627-1.55540884518-4.01814848366.424693258161.906755479247.29724585935-0.2363210536281.152516581860.509893800084-0.683198736355-0.5266834911710.916819734148-0.859604080913-0.7765270082550.8031659337650.8641330036770.0406435376703-0.4340964700761.14083724034-0.2002937373541.0429018044723.742399984952.7575863201-19.4080531343
32.60820935602-2.243320532590.1255425936752.91068782171-0.6927611869713.285203286310.03329149931170.83821065803-0.10915786294-0.78607535963-0.3216559721550.685005906850.0561007631117-0.7459121950720.33690088120.837148884316-0.0261809129879-0.3055158838981.11279657294-0.3683086386781.0516028040219.686471232245.2576799323-25.2352362003
41.251420255431.48445953127-1.628958613533.79026619193-2.729540383742.44934117695-0.999749178121-1.84622992971.033305911450.1632394003230.3966486840520.386146468134-0.8110986731860.03254593000910.5771742507971.438312652-0.0377848392778-0.3747158793492.24096860647-0.4246456362321.3640941099310.770533466936.1786218289-27.8968400447
51.30040194411-1.475029761160.8943559975596.94588024029-2.887954061676.35710736251-0.7396290781210.4431698936-0.425467351619-1.343861585770.6136872194630.804615499028-0.0472502983614-1.115032441221.655596769041.14605526847-0.102269559127-0.7137267004941.59118093625-0.8386875876380.95735501472117.568249157640.7590345824-28.3474843222
62.11401266583-0.7314437274061.084825429596.5680545196-2.925221130261.58139805318-0.07550107483720.783566394057-0.99436509206-1.60982007977-0.4605409391410.4788827670840.282945426276-0.3191963908140.3735973596241.2884615287-0.250004420598-0.1530371060791.4862444978-0.4751818668721.0491430451923.883949986834.6498540871-30.2865565378
71.29372967153-0.6886110549140.1661522218596.75580219858-0.315591865211.75023506559-0.469461644840.445113469171-0.802724968824-0.059670145381-0.3738551823960.7223829477690.917080448503-1.00596450310.6773651643781.19153749623-0.3216202191890.0946502787251.12374261895-0.6431289328131.3462667699623.821126347925.4649055359-16.8168698357
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 50 )-2 - 501 - 53
22chain 'A' and (resid 51 through 98 )51 - 9854 - 82
33chain 'A' and (resid 99 through 126 )99 - 12683 - 110
44chain 'A' and (resid 127 through 138 )127 - 138111 - 122
55chain 'A' and (resid 139 through 149 )139 - 149123 - 133
66chain 'A' and (resid 150 through 164 )150 - 164134 - 148
77chain 'A' and (resid 165 through 195 )165 - 195149 - 179

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