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- PDB-8t5v: Influenza PA-N Endonuclease A36V mutant with Baloxavir -

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Basic information

Entry
Database: PDB / ID: 8t5v
TitleInfluenza PA-N Endonuclease A36V mutant with Baloxavir
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / Influenza endonuclease / resistance / drug discovery / metal-binding pharmacophore / ANTIVIRAL PROTEIN / HYDROLASE-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
Baloxavir acid / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsKohlbrand, A.J. / Cohen, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Biochemistry / Year: 2024
Title: Structural Studies of Inhibitors with Clinically Relevant Influenza Endonuclease Variants.
Authors: Kohlbrand, A.J. / Stokes, R.W. / Sankaran, B. / Cohen, S.M.
History
DepositionJun 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release

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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)23,0464
Polymers22,4531
Non-polymers5933
Water90150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.724, 74.724, 121.619
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 22452.602 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: A36V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Strain: A/California/04/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-E4Z / Baloxavir acid


Mass: 483.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19F2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 306 K / Method: vapor diffusion, hanging drop
Details: 32% PEG (MW 4000 g/mol), 100 mM Tris (pH 8.35), and 220 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→64.76 Å / Num. obs: 16971 / % possible obs: 100 % / Redundancy: 33.3 % / Biso Wilson estimate: 44.49 Å2 / CC1/2: 1 / Net I/σ(I): 17
Reflection shellResolution: 1.79→1.81 Å / Num. unique obs: 2053 / CC1/2: 0.392

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→64.71 Å / SU ML: 0.3048 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.7019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2835 1619 9.54 %
Rwork0.2323 15352 -
obs0.2372 16971 86.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.3 Å2
Refinement stepCycle: LAST / Resolution: 1.79→64.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 36 50 1532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791513
X-RAY DIFFRACTIONf_angle_d1.41572039
X-RAY DIFFRACTIONf_chiral_restr0.0646216
X-RAY DIFFRACTIONf_plane_restr0.0106257
X-RAY DIFFRACTIONf_dihedral_angle_d19.5625557
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.837680.791955X-RAY DIFFRACTION4.04
1.84-1.90.488540.4058549X-RAY DIFFRACTION37.57
1.9-1.970.44091420.41011345X-RAY DIFFRACTION92.94
1.97-2.050.39871510.36431429X-RAY DIFFRACTION100
2.05-2.140.32871530.32751453X-RAY DIFFRACTION99.88
2.14-2.260.35181540.30561460X-RAY DIFFRACTION99.88
2.26-2.40.321540.27951452X-RAY DIFFRACTION99.94
2.4-2.580.34591550.29521471X-RAY DIFFRACTION99.94
2.58-2.840.34941560.26951473X-RAY DIFFRACTION100
2.84-3.250.34511580.25341504X-RAY DIFFRACTION100
3.25-4.10.271610.1941517X-RAY DIFFRACTION100
4.1-64.710.21911730.19171644X-RAY DIFFRACTION99.94
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)
12.763590325965.620171730030.2154404509532.49669247456-0.6613107888955.2541691077-0.3447577713110.914040066355-1.14121046731-0.7565463903-0.0131758358810.01107828142250.8320319921590.160410824130.1552246514140.5403287147930.1170855294890.08821417210090.438355183152-0.1321821106710.57596581242335.30912166485.97069560271-17.3538539791
29.361395258170.683759409374-0.3294430510458.07483012766-4.172883464197.89095052616-0.3778477761931.1263101169-0.310605623937-0.8989136292310.1827932425290.6858757611450.477429647535-0.5486323771050.3175543291840.379373916690.0481756886739-0.01756397745920.476342226299-0.1369036921480.37004642482624.76693370378.69485939273-22.4985216142
39.163333646641.05973830653-6.413016457863.20125915447-0.6914086546192.91793839964-0.3028773078990.313423421339-0.4440025367220.0282267183414-0.0187143139473-0.2669009946050.121699829508-0.6171961715050.1891927199890.3505581468560.0060084300742-0.0196504770590.333590039755-0.03390908729880.29871580329425.501594766610.2703279199-10.9040948855
45.78878068333-2.278683564732.002640057633.759175775613.630437192368.502192919220.364095452254-0.963133692419-0.191233375561-0.203654461837-0.141355323090.1044487335880.0630423477052-0.29498743781-0.2886386091820.392063504342-0.1036184368170.08481826769030.73158689639-0.02339704914490.372863905058.547107946799.17718402027-9.68384831381
54.182307809161.533148168620.3228337323922.80848521323-1.239055891612.225089496240.36690149846-0.643951747850.04894920235360.189447571264-0.1752954272170.369346404283-0.134975809132-0.407869060295-0.1140456337870.3743874975710.07486517204590.06276675974340.539278500133-0.08440519254290.4038350836613.917096430617.0422708752-5.95415763749
67.51342416037-4.855585847974.061807137152.46927281668-2.148890279422.5946072311-0.102739398695-0.08878107749941.25132829901-0.349225447725-0.455898787021-0.223050582526-0.437322211249-0.4474759792140.6403231396190.5882615984060.03745382793560.02340560345310.519312264287-0.08588114271450.58229606130520.768859486627.3679813297-8.53465053989
73.650435392344.28610447278-3.302005603484.73303732226-3.709740192616.44799513858-0.935786669483-0.3928985348970.4820678486150.5570580319890.9262585784880.819297029191-0.920394066277-1.17389468641-0.01371988454420.5473155513530.132831006101-0.01117868256170.511738592131-0.09963558896790.49888939005416.303599727222.2595548538-4.09368282769
88.173423766161.26677539504-2.436428042935.04659345603-1.809139472394.495260596360.154970751037-1.166372907590.3745104503261.06311864292-0.256699577344-0.0508486128473-0.630641454063-0.3449766735380.04110886075440.5282566619590.0442863935392-0.001394479717960.517819622456-0.1044798583970.35939552625423.226051350820.04666992862.12030129029
94.782534240060.728492362753-2.405625676476.60132238908-1.733877384568.73207467716-0.0573758488587-0.667759697959-0.5316008347620.198365149528-0.1935646565550.2343451365960.1779076190490.1887996263910.2106808727970.2865892236220.0434761011722-0.002161851666870.2716234403410.001188399544440.26106498380834.074684863711.613953644-2.890970349
103.965317299670.3340553967060.4087836096022.81874615514-6.447919566025.58420266256-0.164301512561-0.136585417343-0.1090904906710.129605084150.000138895906542-0.0703613819501-0.36770344751-0.1012458641110.2674319127880.3875122065550.06157618276670.02630152852730.343641217783-0.002731062669810.28236276429336.952687420120.8743305711-15.3000149871
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 10 )-1 - 101 - 12
22chain 'A' and (resid 11 through 31 )11 - 3113 - 33
33chain 'A' and (resid 32 through 50 )32 - 5034 - 52
44chain 'A' and (resid 51 through 98 )51 - 9853 - 78
55chain 'A' and (resid 99 through 126 )99 - 12679 - 106
66chain 'A' and (resid 127 through 138 )127 - 138107 - 118
77chain 'A' and (resid 139 through 149 )139 - 149119 - 129
88chain 'A' and (resid 150 through 164 )150 - 164130 - 144
99chain 'A' and (resid 165 through 185 )165 - 185145 - 165
1010chain 'A' and (resid 186 through 197 )186 - 197166 - 177

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