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- PDB-8t67: Influenza PA-N Endonuclease I38T Mutant (amino acids 52-74 truncation) -

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Basic information

Entry
Database: PDB / ID: 8t67
TitleInfluenza PA-N Endonuclease I38T Mutant (amino acids 52-74 truncation)
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / HYDROLASE / Influenza endonuclease / resistance / drug discovery / metal-binding pharmacophore
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
: / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 15, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 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)22,5223
Polymers22,4121
Non-polymers1102
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.589, 74.589, 119.534
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-421-

HOH

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Components

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


Mass: 22412.494 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: I38T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.45 %
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: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→64.62 Å / Num. obs: 22347 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 48.31 Å2 / CC1/2: 0.999 / Net I/σ(I): 18
Reflection shellResolution: 2.08→2.13 Å / Num. unique obs: 1068 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→64.6 Å / SU ML: 0.3162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2481 2245 10.05 %
Rwork0.2061 20102 -
obs0.2103 22347 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.72 Å2
Refinement stepCycle: LAST / Resolution: 2.08→64.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 2 48 1506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541493
X-RAY DIFFRACTIONf_angle_d0.8232006
X-RAY DIFFRACTIONf_chiral_restr0.0527214
X-RAY DIFFRACTIONf_plane_restr0.008257
X-RAY DIFFRACTIONf_dihedral_angle_d19.3613566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.39081380.32661266X-RAY DIFFRACTION99.86
2.13-2.170.33961420.28791244X-RAY DIFFRACTION99.86
2.17-2.230.41811470.26711245X-RAY DIFFRACTION99.93
2.23-2.290.30031400.25911234X-RAY DIFFRACTION99.71
2.29-2.360.28071430.25821266X-RAY DIFFRACTION99.93
2.36-2.430.30631350.25741263X-RAY DIFFRACTION100
2.43-2.520.29971350.25521265X-RAY DIFFRACTION100
2.52-2.620.29881420.2521247X-RAY DIFFRACTION100
2.62-2.740.34411450.23051246X-RAY DIFFRACTION100
2.74-2.880.27651430.24151275X-RAY DIFFRACTION100
2.88-3.060.31111380.24631256X-RAY DIFFRACTION100
3.07-3.30.28151400.23831246X-RAY DIFFRACTION100
3.3-3.630.21381340.19451262X-RAY DIFFRACTION100
3.63-4.160.1971430.16871268X-RAY DIFFRACTION100
4.16-5.240.19071440.15481249X-RAY DIFFRACTION100
5.24-64.60.23511360.1951270X-RAY DIFFRACTION99.58
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)
12.046278198399.333007254050.03990624076137.895888264830.4992099327342.04000131586-0.5071735711851.01982193559-0.188863204347-0.7462790529460.4902209414850.2813995611830.16162578590.04759438932450.1098939460120.6060575798520.123158178170.02655658703810.623169338099-0.04483687444560.52239279420628.9487.211-20.136
26.043975253860.371063636027-0.3715407375540.926586575802-0.1551450214572.85651719473-0.0467891602555-0.436122728792-0.4639702714310.0689668535648-0.1557221798360.08584162722110.216693058616-0.4562919109160.2175328907010.411258501836-0.01409910229820.09855219524690.341684414164-0.03930287971810.37135507878715.6689.289-9.686
39.104874456162.45648984468-0.6920787300163.85409839396-0.8493349438823.199062863220.278520041454-0.4536989260530.3792785845410.210864677379-0.197557333680.323635586919-0.0528544146015-0.654625221645-0.07173034192290.4044470825040.07037743381370.1048269014390.499937622509-0.06509932498770.39837307801513.20416.902-5.927
44.19129038270.6527421587151.844025819318.03804310182-4.482844509246.61842244896-0.0288404585216-0.3697315164160.6389597063750.224008183948-0.02321497913490.206112805971-0.584157110135-0.5891165582230.1106975320570.4675769460270.05649033796670.1289678140490.345593124084-0.1029454741780.51307720754220.34923.245-3.41
57.548898589591.190323164381.388200265995.69045361911-1.145749243538.517175541960.1820575102490.114298116162-0.0518620830337-0.182116294841-0.394885789262-0.07602364486290.07170810903430.4159985903280.1497103287820.3127031260540.05506431786460.02405654898310.187066473434-0.01371956432930.27009888138334.60414.53-7.047
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:31 )A-1 - 31
2X-RAY DIFFRACTION2( CHAIN A AND RESID 32:98 )A32 - 98
3X-RAY DIFFRACTION3( CHAIN A AND RESID 99:126 )A99 - 126
4X-RAY DIFFRACTION4( CHAIN A AND RESID 127:164 )A127 - 164
5X-RAY DIFFRACTION5( CHAIN A AND RESID 165:195 )A165 - 195

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