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- PDB-9pmr: Influenza PA-N Endonuclease I38T mutant with compound 2 ((6M)-6-(... -

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Basic information

Entry
Database: PDB / ID: 9pmr
TitleInfluenza PA-N Endonuclease I38T mutant with compound 2 ((6M)-6-(2-ethylphenyl)-3,4-dihydroxypyridine-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
: / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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)22,6924
Polymers22,3221
Non-polymers3693
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-7 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.671, 75.671, 119.472
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-314-

HOH

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Components

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


Mass: 22322.371 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-A1CI3 / (6M)-6-(2-ethylphenyl)-3,4-dihydroxypyridine-2-carboxylic acid


Mass: 259.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG4000 g/mol, 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→37.84 Å / Num. obs: 14328 / % possible obs: 99.9 % / Redundancy: 38.6 % / Biso Wilson estimate: 55.75 Å2 / CC1/2: 0.997 / Net I/σ(I): 35.7
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 1371 / CC1/2: 0.294

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→37.84 Å / SU ML: 0.3159 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2516 1016 10.01 %
Rwork0.2083 9138 -
obs0.2126 10154 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.04 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1456 0 21 24 1501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511509
X-RAY DIFFRACTIONf_angle_d0.77742028
X-RAY DIFFRACTIONf_chiral_restr0.0508214
X-RAY DIFFRACTIONf_plane_restr0.0084259
X-RAY DIFFRACTIONf_dihedral_angle_d21.2427568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.370.35811400.27991261X-RAY DIFFRACTION99.93
2.37-2.520.28811410.2521264X-RAY DIFFRACTION100
2.52-2.710.34541420.26181281X-RAY DIFFRACTION100
2.71-2.980.26531430.25261281X-RAY DIFFRACTION100
2.98-3.420.32031430.24421298X-RAY DIFFRACTION100
3.42-4.30.24971470.19571322X-RAY DIFFRACTION100
4.3-37.840.20491600.17931431X-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)
16.826091170443.233657084112.349650473143.335795084942.101696476546.217858282290.1740184928811.22712767204-0.6866865730010.05246078453790.115569550265-0.1762407840270.1035234440550.350172599481-0.3929912447780.7048909328990.05233152182040.1238322478530.586991423878-0.1264940365640.57151352431829.66107502277.18888378334-20.459099181
29.6052010806-0.050618772461-1.539919176371.778709016580.1119128117852.51132183081-0.118718443409-0.388943741402-0.5951779769520.174201988521-0.07593049423270.2221544567450.116044156506-0.1748612112720.2065347075910.555011717491-0.004368731822410.05608226486170.388073214126-0.004884252341060.45602627056815.090434605912.8085280147-8.16741684964
38.94845218411-1.38384629816-0.9494900707731.86775356911-0.8352566864872.627775608720.149042647188-0.1548125647990.4921841992710.194764039848-0.06484474654660.309934203008-0.4734653696660.0523807575186-0.1215277575220.648598459541-0.03863141597260.03597558558330.302925082838-0.04657132994450.43263665875327.463573416819.5080384479-4.95662967461
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 31 )B-1 - 312 - 34
22chain 'A' and (resid 32 through 126 )B32 - 12635 - 109
33chain 'A' and (resid 127 through 198 )B - D127 - 302110

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