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- PDB-8t5z: Influenza PA-N Endonuclease (amino acids 52-74 truncation) -

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Basic information

Entry
Database: PDB / ID: 8t5z
TitleInfluenza PA-N Endonuclease (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 / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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: 2.03 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 1.0May 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)22,5343
Polymers22,4251
Non-polymers1102
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.820, 75.820, 122.262
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-411-

HOH

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Components

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


Mass: 22424.547 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-198)
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 / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
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: 2.03→65.7 Å / Num. obs: 25379 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 44.41 Å2 / CC1/2: 1 / Net I/σ(I): 24
Reflection shellResolution: 2.03→2.1 Å / Num. unique obs: 1362 / CC1/2: 0.785

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→65.66 Å / SU ML: 0.3007 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4762
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 2533 9.98 %
Rwork0.222 22846 -
obs0.2247 25379 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.98 Å2
Refinement stepCycle: LAST / Resolution: 2.03→65.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 2 46 1511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291496
X-RAY DIFFRACTIONf_angle_d0.55932009
X-RAY DIFFRACTIONf_chiral_restr0.0415215
X-RAY DIFFRACTIONf_plane_restr0.0033257
X-RAY DIFFRACTIONf_dihedral_angle_d19.8715569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.070.471400.37811272X-RAY DIFFRACTION99.72
2.07-2.110.34471430.30521277X-RAY DIFFRACTION99.58
2.11-2.160.27871390.27931261X-RAY DIFFRACTION99.72
2.16-2.210.33181400.25561253X-RAY DIFFRACTION100
2.21-2.260.30921410.24971275X-RAY DIFFRACTION99.93
2.26-2.320.2531390.25381267X-RAY DIFFRACTION99.79
2.32-2.390.2851480.25631275X-RAY DIFFRACTION100
2.39-2.470.31541370.2711271X-RAY DIFFRACTION99.65
2.47-2.560.34941390.25771272X-RAY DIFFRACTION99.79
2.56-2.660.37271420.25941253X-RAY DIFFRACTION99.86
2.66-2.780.32861350.25651283X-RAY DIFFRACTION99.86
2.78-2.930.33251370.25431287X-RAY DIFFRACTION99.93
2.93-3.110.25471410.25691252X-RAY DIFFRACTION99.71
3.11-3.350.30641370.24351270X-RAY DIFFRACTION99.65
3.35-3.690.22051420.2111266X-RAY DIFFRACTION99.79
3.69-4.220.18361410.17711277X-RAY DIFFRACTION99.44
4.22-5.320.19311490.17441256X-RAY DIFFRACTION100
5.32-65.660.20811430.20981279X-RAY DIFFRACTION99.79
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)
19.862566048194.97714359925-0.6638458162885.30286044988-0.6454545337119.41056118122-0.3108875644921.15992563002-0.38124741392-0.8645281882140.3224916627760.09093909267950.103291985272-0.149366433611-0.03140432537630.5934478295510.0387235080015-0.0001380976842770.40878583926-0.1004975301390.41041477700729.50173209237.64966951286-20.2064704857
25.961545649430.530942223005-0.6315833919661.841434728070.3949134235392.174526020470.0260447579358-0.201905571104-0.07107623654510.0244062889104-0.05994518280040.3698191802960.0655802052253-0.195565551460.03367847806070.403743623586-0.002372295680710.01978015330470.3075319693980.03897505124990.38169284599215.256597320513.2192344719-8.54567460318
36.97227018478-0.82048609617-1.028685272213.1567388770.1031011263313.417858461020.193770126396-0.182848204140.2770098563710.0673531691892-0.1621134898710.18787615107-0.2355363563080.106765561795-0.04341813141920.410094506136-0.0556273443925-0.0120813568980.265286026494-0.008957701544930.29233298371827.686290682619.8662891511-5.37694898854
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 31 )-1 - 311 - 33
22chain 'A' and (resid 32 through 126 )32 - 12634 - 107
33chain 'A' and (resid 127 through 196 )127 - 196108 - 177

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