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- PDB-9fxv: Influenza polymerase A C-terminal domain of PA subunit with pepti... -

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Basic information

Entry
Database: PDB / ID: 9fxv
TitleInfluenza polymerase A C-terminal domain of PA subunit with peptide inhibitor containing two norleucines
Components
  • Peptide inhibitor
  • Polymerase acidic protein
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 / hydrolase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription ...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 / hydrolase activity / 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
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4984
Polymers54,2422
Non-polymers2562
Water3,819212
1
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1963
Polymers52,9401
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)1,3021
Polymers1,3021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.857, 119.561, 123.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
Details: ...Details: SIEPFLRTTPRPLRLPDGPLCHQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIVKPHEKGINPNYLMAWKQVLAELQDIENEEKIPRTKNMKRTSQLKWALGENMAPEKVDFDDCKDVGDLKQYDSDEPEPRSLASWVQNEFNKACELTDSSWIELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDMTKEFFENKSETWPIGESPRGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALK
Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1))
Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C3W5X6, Hydrolases; Acting on ester bonds
#2: Protein/peptide Peptide inhibitor / ASP-TYR-ASN-PRO-TYR-NLE-LEU-TYR-NLE-LYS


Mass: 1302.495 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Peptide inhibitor containing two norleucines derived from the optimized small peptide inhibitor in entry 7ZPY
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
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: 2.58 Å3/Da / Density % sol: 52.32 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.3→26.91 Å / Num. obs: 24417 / % possible obs: 95 % / Redundancy: 3.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.044 / Rrim(I) all: 0.086 / Χ2: 0.86 / Net I/σ(I): 9.9
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 66.2 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.833 / Num. measured all: 2437 / Num. unique obs: 1630 / CC1/2: 0.615 / Rpim(I) all: 0.752 / Rrim(I) all: 1.126 / Χ2: 0.57 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→26.91 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.925 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27948 432 1.8 %RANDOM
Rwork0.24192 ---
obs0.2426 23928 94.52 %-
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: 56.869 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å2-0 Å2-0 Å2
2---1.98 Å2-0 Å2
3---0.91 Å2
Refinement stepCycle: 1 / Resolution: 2.3→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 17 212 3564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123425
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163196
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.6544620
X-RAY DIFFRACTIONr_angle_other_deg0.4991.5717361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.641517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61110551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023953
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
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_it7.0356.3771715
X-RAY DIFFRACTIONr_mcbond_other7.0346.3771715
X-RAY DIFFRACTIONr_mcangle_it9.45811.4152123
X-RAY DIFFRACTIONr_mcangle_other9.45511.4182124
X-RAY DIFFRACTIONr_scbond_it6.8796.5061710
X-RAY DIFFRACTIONr_scbond_other6.8776.5071711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.82211.8322498
X-RAY DIFFRACTIONr_long_range_B_refined12.81962.233852
X-RAY DIFFRACTIONr_long_range_B_other12.81762.233853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 26 -
Rwork0.359 1144 -
obs--62.1 %

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