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- PDB-9pmp: Influenza PA-N Endonuclease I38T mutant with compound 1 (3-hydrox... -

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Basic information

Entry
Database: PDB / ID: 9pmp
TitleInfluenza PA-N Endonuclease I38T mutant with compound 1 (3-hydroxy-6-(2-methylphenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid)
ComponentsPolymerase acidic protein
KeywordsLYASE / Metal binding protein / endonuclease / influenza endonuclease
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
Chem-HNS / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsKohlbrand, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI149444 United States
CitationJournal: J.Inorg.Biochem. / Year: 2025
Title: Substituent size versus metal binding of inhibitors with variants of influenza endonuclease.
Authors: Kohlbrand, A.J. / Stokes, R.W. / Sankaran, B. / Cohen, S.M.
History
DepositionJul 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: 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)22,7684
Polymers22,4121
Non-polymers3553
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-7 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.809, 74.809, 118.947
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

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Components

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


Mass: 22412.494 Da / Num. of mol.: 1 / Mutation: I38T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (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-HNS / 3-hydroxy-6-(2-methylphenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid


Mass: 245.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 34% PEG4000, 100 mM Tris, pH 8.35, 220 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→37.4 Å / Num. obs: 7367 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 64.69 Å2 / CC1/2: 1 / Net I/σ(I): 11.5
Reflection shellResolution: 2.49→2.68 Å / Num. unique obs: 700 / CC1/2: 0.902

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→37.4 Å / SU ML: 0.3253 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2659 737 10 %
Rwork0.2222 6630 -
obs0.2267 7367 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.54 Å2
Refinement stepCycle: LAST / Resolution: 2.49→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 20 1 1481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531513
X-RAY DIFFRACTIONf_angle_d0.69842034
X-RAY DIFFRACTIONf_chiral_restr0.0414214
X-RAY DIFFRACTIONf_plane_restr0.0069260
X-RAY DIFFRACTIONf_dihedral_angle_d21.9155569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.680.33141410.30761269X-RAY DIFFRACTION98.95
2.68-2.950.32681430.28571290X-RAY DIFFRACTION100
2.95-3.380.3561450.281301X-RAY DIFFRACTION99.79
3.38-4.250.27351480.22421332X-RAY DIFFRACTION100
4.26-37.40.22121600.18591438X-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)
14.637868958393.977145914222.742698513964.227156402071.569001337822.27151506108-0.481588556490.87878596454-0.441364674023-0.2224803357220.593536605989-0.0377091811318-0.1051329152490.3482085715140.02114692537850.774746875928-0.03028535410210.2110480639370.6297538656-0.1977783047050.72621920054529.2277.305-20.216
24.51869499422-3.72089014351-3.687303876877.667434948772.819041642444.51182235149-0.5412934079580.272790905393-0.234964331344-0.321452565430.1837396816550.4478722409050.325316320951-1.145636480940.2587997864620.618941385419-0.049432485198-0.04784039571050.4726618260070.0491813188940.4902584471525.38610.246-10.868
34.42261749354-2.14507947494-3.329074926724.651025838650.9140523256115.509414451140.484606190413-0.445856930837-0.259088630382-0.1454974307290.1886055819410.3097870087410.1971855982820.581044739351-0.09783523744280.512793408257-0.03873046492310.07134931511020.71424280952-0.01502803971550.63012374113314.2667.267-5.543
46.136561802082.145321178070.6564660345593.03523477341-0.5289279053664.533322184190.4580235623640.1648928931220.02796379009930.0536250442643-0.0542003916934-0.1740178479380.0908469711526-0.4472011456-0.3309787517390.6027293555290.0920972510230.1531493116180.438067194057-0.0341582993680.48106708222510.6415.019-7.951
54.97754895183-1.046026230360.7717003894753.91524828182-4.356324010115.01573021477-0.013830700004-0.1580214479130.2818467108130.2531484748650.2274104135050.5232466358920.0464099950521-0.8675176916050.144937325590.681616067995-0.05470919471540.1033388138950.59841671055-0.1196651009330.74778035337818.73425.068-6.44
66.69147147160.230305807088-3.016579555611.064078269370.2587731771897.29204519105-0.0609379656192-0.3836749781530.06351131615330.276600661915-0.2432076137560.1545367017650.157538663510.2881446024060.4073170036360.603335891975-0.0023267531979-0.01332644772910.353948744963-0.05350021587110.54523481549331.64416.249-4.053
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 32:50 )A32 - 50
3X-RAY DIFFRACTION3( CHAIN A AND RESID 51:83 )A51 - 83
4X-RAY DIFFRACTION4( CHAIN A AND RESID 84:126 )A84 - 126
5X-RAY DIFFRACTION5( CHAIN A AND RESID 127:149 )A127 - 149
6X-RAY DIFFRACTION6( CHAIN A AND RESID 150:195 )A150 - 195

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