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- PDB-7zpy: Influenza polymerase A C-terminal domain of PA subunit with optim... -

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Basic information

Entry
Database: PDB / ID: 7zpy
TitleInfluenza polymerase A C-terminal domain of PA subunit with optimized small peptide inhibitor
Components
  • Peptide inhibitor (ASP-TYR-ASN-PRO-TYR-LEU-LEU-TYR-LEU-LYS)
  • Polymerase acidic protein
KeywordsVIRAL PROTEIN / antiviral peptides / Influenza A polymerase / protein-protein interaction
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 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
METHOXY-ETHOXYL / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRadilova, K. / Brynda, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729European Union
CitationJournal: Antiviral Res. / Year: 2022
Title: Thermodynamic and structural characterization of an optimized peptide-based inhibitor of the influenza polymerase PA-PB1 subunit interaction.
Authors: Radilova, K. / Zima, V. / Kral, M. / Machara, A. / Majer, P. / Hodek, J. / Weber, J. / Brynda, J. / Strmen, T. / Konvalinka, J. / Kozisek, M.
History
DepositionApr 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 (ASP-TYR-ASN-PRO-TYR-LEU-LEU-TYR-LEU-LYS)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3173
Polymers54,2422
Non-polymers751
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-16 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.850, 122.210, 123.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
Source: (gene. exp.) Influenza A virus (A/California/07/2009(H1N1))
Strain: 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-LEU-LEU-TYR-LEU-LYS)


Mass: 1302.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MOE / METHOXY-ETHOXYL


Mass: 75.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
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: 0.91841 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.72→39.04 Å / Num. obs: 46317 / % possible obs: 99.5 % / Redundancy: 6.815 % / Biso Wilson estimate: 41.616 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.102 / Χ2: 0.77 / Net I/σ(I): 9.8 / Num. measured all: 820273
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.72-1.827.062.5320.5413797819548195440.2812.734100
1.82-1.956.8331.4191.0812405418405181550.731.53898.6
1.95-2.16.6350.7012.1511318717063170600.8040.76100
2.1-2.316.9180.414.4410688515763154500.940.44498
2.31-2.586.8530.2068.219773314263142610.9790.223100
2.58-2.976.9760.11615.228755212554125510.9930.125100
2.97-3.646.6580.07225.677050010592105890.9970.078100
3.64-5.136.3710.0513552163820281870.9980.05599.8
5.13-39.046.6260.03838.9630221457045610.9990.04199.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6SYI

6syi


Resolution: 1.9→39.04 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2386 / WRfactor Rwork: 0.1924 / FOM work R set: 0.824 / SU B: 3.77 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1368 / SU Rfree: 0.1322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 808 1.7 %RANDOM
Rwork0.1955 ---
obs0.1962 45509 97.57 %-
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 max: 127.72 Å2 / Biso mean: 42.591 Å2 / Biso min: 24.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0 Å2
2---1.31 Å20 Å2
3---1.49 Å2
Refinement stepCycle: final / Resolution: 1.9→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 5 273 3832
Biso mean--52.98 46.25 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133753
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153558
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.6485103
X-RAY DIFFRACTIONr_angle_other_deg1.31.5778229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1565479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03222.398196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8315679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1051525
X-RAY DIFFRACTIONr_chiral_restr0.0670.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024237
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02853
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 42 -
Rwork0.549 2412 -
all-2454 -
obs--70.62 %

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