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

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Basic information

Entry
Database: PDB / ID: 7mpf
TitleThe crystal structure of wild type PA endonuclease (2009/H1N1/CALIFORNIA) in complex with SJ000986436
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / Hydrolase / NUCLEASE / INFLUENZA / INHIBITOR RESISTANCE / VIRAL PROTEIN-Inhibitor complex
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Polymerase acidic protein / 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-R1D / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCuypers, M.G. / Slavish, J.P. / 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
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 22, 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

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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)24,4736
Polymers23,1481
Non-polymers1,3245
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.723, 89.723, 133.700
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 / RNA-directed RNA polymerase subunit P2


Mass: 23148.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain swl A/California/04/2009 H1N1)
Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 13 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-R1D / 5-hydroxy-N-[2-(4-hydroxy-3-methoxyphenyl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-1,6-dihydropyrimidine-4-carboxamide


Mass: 449.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H18F3N3O5 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#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.: 8 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
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: Mar 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→74.5 Å / Num. obs: 7817 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 58 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.046 / Χ2: 0.63 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 987 / CC1/2: 0.759 / Rpim(I) all: 0.422 / Χ2: 0.63 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VL3

6vl3


Resolution: 2.8→74.5 Å / SU ML: 0.4544 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.8774
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2439 369 5.26 %
Rwork0.223 6645 -
obs0.2241 7014 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.67 Å2
Refinement stepCycle: LAST / Resolution: 2.8→74.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1415 0 87 8 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221571
X-RAY DIFFRACTIONf_angle_d0.51512134
X-RAY DIFFRACTIONf_chiral_restr0.0387218
X-RAY DIFFRACTIONf_plane_restr0.0033268
X-RAY DIFFRACTIONf_dihedral_angle_d19.7292554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.39371150.29732171X-RAY DIFFRACTION99.91
3.21-4.040.27481310.22342179X-RAY DIFFRACTION99.96
4.04-74.50.1921230.20092295X-RAY DIFFRACTION98.98
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)
14.78398171704-0.23259371931-3.211446711341.39977434385-1.057772815456.270747216320.01387620889410.6888686942690.268483660672-0.0938486263787-0.315373978996-0.198759848027-0.84151610521-0.0774568547420.2286426495480.689040046906-0.102947596412-0.2686156614270.5000754584610.01628390328510.5565576746049.8940587229624.07499664137.57810352145
25.48643213859-0.7557006432240.4622440941681.68790829372-1.593161827726.056533658580.1493026499580.2120602063660.2358694016630.786101145982-0.5574331685270.177008121827-0.461681590265-1.070028348230.3840679640290.8863029893860.0439727174663-0.1812866826910.69715781982-0.2941007261010.4740885747-7.289373287821.599488950219.2625178803
33.26695169775-1.963128995990.2897304904992.183318416390.3168523695942.96299669488-0.0937104181147-0.8437590434820.940043377550.530382766781-0.09435150609270.110416401965-0.7073331856680.341515915790.1865884945810.920583279147-0.0134691368839-0.277462838380.683068037629-0.2531341206740.5251607705730.25753872737325.659101836924.9820420447
44.965085498161.18110261916-1.137010944751.312536260161.804970508814.584281505340.143037410057-0.4349840462660.2974155877020.4373059979270.867831696262-1.1403923988-0.7850897871310.73050680405-0.8472528518891.83208440186-0.257491668919-0.2493228885430.889918246475-0.2653165675680.96621311412110.175579672133.891059739427.6007849038
54.12269695857-3.13338544175-4.270524846772.517629143772.459831676978.965931207570.488392663389-0.7397718520090.3358514637080.313150730664-0.308855796772-0.266060592025-0.568924783495-0.3229351513830.2324028326620.821746910273-0.199449415872-0.2173039245350.785835565492-0.2762709116360.567141806474.6218006082727.617480819928.1408483793
63.34746217234-0.359526570316-1.067119471881.07599553675-1.649477968373.822650674980.0617957586919-0.3188323031290.2159087129310.474903838692-0.312003640792-0.379719282325-0.944375830290.5768778441290.2862620131960.816548429773-0.199497923284-0.3415630776030.6693851011770.01881732208790.6226430641817.214436778421.377031375620.7774575128
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 -3 through 50 )-3 - 501 - 54
22chain 'A' and (resid 51 through 98 )51 - 9855 - 83
33chain 'A' and (resid 99 through 126 )99 - 12684 - 111
44chain 'A' and (resid 127 through 137 )127 - 137112 - 122
55chain 'A' and (resid 138 through 149 )138 - 149123 - 134
66chain 'A' and (resid 150 through 195 )150 - 195135 - 180

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