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- PDB-9fxx: Influenza polymerase A C-terminal domain of PA subunit with stapl... -

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Basic information

Entry
Database: PDB / ID: 9fxx
TitleInfluenza polymerase A C-terminal domain of PA subunit with stapled peptide inhibitor
Components
  • Polymerase acidic protein
  • Stapled peptide inhibitor
KeywordsVIRAL PROTEIN / influenza A RNA-dependent RNA polymerase / protein-protein interaction / peptide inhibitor
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
: / TRIETHYLENE GLYCOL / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsRadilova, K. / Brynda, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: To Be Published
Title: Influenza polymerase A C-terminal domain of PA subunit
Authors: Radilova, K. / Zima, V. / Brynda, J. / Konvalinka, J. / Machara, A. / Kozisek, M.
History
DepositionJul 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: 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
B: Stapled peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5536
Polymers54,2222
Non-polymers3304
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-9 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.019, 118.797, 123.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 52939.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1))
Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds
#2: Protein/peptide Stapled peptide inhibitor


Mass: 1282.465 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Stapled peptide inhibitor derived from the optimized small peptide inhibitor in entry 7ZPY
Source: (synth.) Influenza A virus (A/California/07/2009(H1N1))

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Non-polymers , 4 types, 57 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-A1IG4 / (E)-but-2-ene


Mass: 56.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M MOPS/HEPES; 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 30962 / % possible obs: 99.9 % / Redundancy: 13.12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.126 / Net I/σ(I): 15.83
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.16-2.293.06149070.443.181
2.29-2.451.69346070.721.7591
2.45-2.641.00243360.8481.0441
2.64-2.890.49439930.960.5131
2.89-3.230.24436270.9890.2541
3.23-3.730.10332320.9980.1071
3.73-4.560.0527610.9990.0521
4.56-6.410.04122000.9990.0431
6.41-100.027131810.0281

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→42.9 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.031 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27683 1550 5 %RANDOM
Rwork0.21931 ---
obs0.22215 29477 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 69.074 Å2
Baniso -1Baniso -2Baniso -3
1-2.62 Å2-0 Å20 Å2
2---1.38 Å20 Å2
3----1.24 Å2
Refinement stepCycle: 1 / Resolution: 2.16→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 14 53 3427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123448
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163220
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.8364662
X-RAY DIFFRACTIONr_angle_other_deg0.4981.7557413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5935428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.675518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54910579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02771
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.5877.4841724
X-RAY DIFFRACTIONr_mcbond_other5.5787.4851724
X-RAY DIFFRACTIONr_mcangle_it8.07713.4322148
X-RAY DIFFRACTIONr_mcangle_other8.07513.4342149
X-RAY DIFFRACTIONr_scbond_it6.3457.5581724
X-RAY DIFFRACTIONr_scbond_other6.3447.5581725
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.45913.7732515
X-RAY DIFFRACTIONr_long_range_B_refined11.99769.783750
X-RAY DIFFRACTIONr_long_range_B_other11.99969.83747
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 110 -
Rwork0.379 2133 -
obs--100 %

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