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- PDB-6syi: C-TERMINAL DOMAIN OF INFLUENZA POLYMERASE PA SUBUNIT AND OPTIMIZE... -

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Basic information

Entry
Database: PDB / ID: 6syi
TitleC-TERMINAL DOMAIN OF INFLUENZA POLYMERASE PA SUBUNIT AND OPTIMIZED SMALL PEPTIDE INHIBITOR
Components
  • PB1-11
  • Polymerase acidic protein
KeywordsVIRAL PROTEIN / neuraminidase / influenza / complex
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 / 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
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsHejdanek, J. / Pachl, P.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: Antiviral Res. / Year: 2020
Title: structural characterization of the interaction between the C-terminal domain of the influenza polymerase PA subunit and an optimized small peptide inhibitor.
Authors: Hejdanek, J. / Radilova, K. / Pachl, P. / Hodek, J. / Machara, A. / Weber, J. / Rezacova, P. / Konvalinka, J. / Kozisek, M.
History
DepositionSep 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
B: PB1-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6257
Polymers54,2262
Non-polymers3985
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint6 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.521, 120.883, 122.626
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/Wisconsin/629-D00036/2009(H1N1))
Gene: PA / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D4HIS2, Hydrolases; Acting on ester bonds
#2: Protein/peptide PB1-11


Mass: 1286.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES; pH 7.5, 35% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→43.043 Å / Num. obs: 74825 / % possible obs: 99.7 % / Redundancy: 6.564 % / Biso Wilson estimate: 35.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.08 / Χ2: 1.112 / Net I/σ(I): 13.42 / Num. measured all: 491165
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
1.6-1.696.2842.6580.667393611980117660.2762.89798.2
1.69-1.816.6231.4431.327444811245112410.6051.565100
1.81-1.966.9380.7522.697301810529105250.8720.812100
1.96-2.146.8050.3485.5865900968696840.970.377100
2.14-2.396.3490.17110.4555823879987930.9910.18699.9
2.39-2.766.6380.09318.4252001783678340.9970.101100
2.76-3.386.7530.05132.4545130668466830.9990.055100
3.38-4.776.0680.0350.9631812524952430.9990.03399.9
4.77-43.0436.2490.02658.4719097307930560.9990.02899.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZNL

2znl


Resolution: 1.6→34.4 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2046 / WRfactor Rwork: 0.1773 / FOM work R set: 0.6984 / SU B: 5.415 / SU ML: 0.09 / SU R Cruickshank DPI: 0.0789 / SU Rfree: 0.0809 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 2101 2.8 %RANDOM
Rwork0.1913 ---
obs0.1922 72724 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.85 Å2 / Biso mean: 38.131 Å2 / Biso min: 19.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å2-0 Å20 Å2
2---1.22 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 1.6→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 26 316 3744
Biso mean--53.02 38.33 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133521
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173267
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.6484762
X-RAY DIFFRACTIONr_angle_other_deg1.4311.5787585
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0435434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65722.37173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3315613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6841521
X-RAY DIFFRACTIONr_chiral_restr0.0730.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02730
LS refinement shellResolution: 1.6→1.639 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.459 149 -
Rwork0.437 5137 -
obs--96.13 %
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)
10.00140.01840.00940.87660.84891.22870.00220.0074-0.00190.00950.0524-0.03-0.12330.0114-0.05450.12770.0206-0.02140.0993-0.02960.0216-9.3672.91232.901
20.42610.06870.01260.93080.03860.34580.00860.016-0.0813-0.1220.02240.00830.07860.0023-0.03090.12640.0168-0.02460.0521-0.00520.0204-13.46-21.1388.895
31.0687-0.21631.22560.98610.45081.937-0.0253-0.0058-0.0063-0.20650.0330.0184-0.17350.0449-0.00770.11270.01-0.04270.0618-0.02250.0269-13.9732.93720.899
40.12070.01420.11050.50070.45890.5319-0.0269-0.0520.0189-0.0872-0.03320.0652-0.0596-0.03790.060.10540.0321-0.04150.0843-0.01070.0236-17.61-10.13115.308
51.08040.0134-0.44480.44690.13810.6074-0.0101-0.05620.0525-0.0671-0.0280.03710.01870.04630.03810.08890.0151-0.02920.0735-0.01660.0244-12.586-8.48415.33
60.6825-0.6320.72624.71710.7021.2558-0.1466-0.28180.151-0.2961-0.27210.5917-0.2779-0.47210.41870.12080.1425-0.13660.2054-0.18690.2351-29.78516.34424.461
70.1095-0.04820.19081.21041.00011.3238-0.06230.0162-0.00650.0434-0.02650.118-0.07650.01360.08880.1320.0062-0.01960.0524-0.02990.0294-15.0369.55836.121
81.0292-2.2529-1.70255.1473.88522.96890.0422-0.04720.0214-0.3101-0.00250.0056-0.24340.0398-0.03960.20080.0604-0.0430.0882-0.04650.0487-12.51511.39827.96
90.0011-0.03140.02617.859-1.99143.86170.006-0.00360.0001-0.09090.01880.2713-0.2273-0.166-0.02480.09720.0067-0.0340.0467-0.03840.0693-16.92818.24132.344
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A256 - 293
2X-RAY DIFFRACTION2A294 - 397
3X-RAY DIFFRACTION3A398 - 443
4X-RAY DIFFRACTION4A444 - 549
5X-RAY DIFFRACTION5A550 - 581
6X-RAY DIFFRACTION6A582 - 615
7X-RAY DIFFRACTION7A616 - 716
8X-RAY DIFFRACTION8B2 - 6
9X-RAY DIFFRACTION9B7 - 11

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