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- PDB-7kaf: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 7kaf
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease I38T (construct with truncated loop 51-72) in complex with baloxavir acid
ComponentsProtein PA-X
KeywordsVIRAL PROTEIN / NUCLEASE / INFLUENZA / cleaved / DNA BINDING PROTEIN
Function / homology
Function and homology information


viral RNA genome replication / RNA binding / metal ion binding
Similarity search - Function
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
Baloxavir acid / : / Hexa Vinylpyrrolidone K15 / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCuypers, M.G. / Kumar, G. / Slavish, J. / White, S.W.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism.
Authors: Kumar, G. / Cuypers, M. / Webby, R.R. / Webb, T.R. / White, S.W.
History
DepositionSep 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: 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: Protein PA-X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5917
Polymers23,1361
Non-polymers1,4546
Water1,11762
1
A: Protein PA-X
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)196,72556
Polymers185,0908
Non-polymers11,63548
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area19220 Å2
ΔGint-338 kcal/mol
Surface area61260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.824, 89.824, 133.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein PA-X


Mass: 23136.289 Da / Num. of mol.: 1 / Mutation: i38T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus, (gene. exp.) Influenza A virus (A/Luxembourg/43/2009(H1N1))
Gene: PA-X, PA / Strain: A/Luxembourg/43/2009(H1N1) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4D6EED0, UniProt: C6H0Y9

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Non-polymers , 5 types, 68 molecules

#2: Chemical ChemComp-E4Z / Baloxavir acid


Mass: 483.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19F2N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-QQ4 / Hexa Vinylpyrrolidone K15 / 1,1',1'',1''',1'''',1'''''-[(3R,5R,7R,9S,11R)-dodecane-1,3,5,7,9,11-hexayl]hexa(pyrrolidin-2-one)


Mass: 668.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H56N6O6
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 10mM MnCl2, 10mM MgCl2, 0.5% Polyvinylpyrrolidone K15

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→46.06 Å / Num. obs: 12419 / % possible obs: 93.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 46 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.032 / Rrim(I) all: 0.104 / Net I/σ(I): 12
Reflection shellResolution: 2.25→2.33 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 762 / CC1/2: 0.679 / Rpim(I) all: 0.332 / Rrim(I) all: 0.744

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.25→46.06 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 697 5.62 %
Rwork0.1923 11711 -
obs0.1948 12408 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.07 Å2 / Biso mean: 60.1328 Å2 / Biso min: 32.26 Å2
Refinement stepCycle: final / Resolution: 2.25→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 104 62 1635
Biso mean--73.53 60.96 -
Num. residues----181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.420.3109860.27711678176468
2.42-2.670.28211440.24562398254297
2.67-3.050.28891690.22092465263499
3.06-3.850.20011390.181125312670100
3.85-46.060.22371590.172126392798100
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)
11.79080.16470.34556.92191.89512.4471-0.32060.16340.1025-0.36830.2681-0.1001-0.22370.60270.01210.2787-0.024-0.07750.54790.17560.326723.1256-2.160314.239
21.5779-2.4245-0.27934.6109-0.23021.8917-0.4896-0.40970.08161.22580.9861-1.42930.04761.52470.44050.39530.2842-0.20910.80650.07150.471929.8353-8.01426.6042
31.5881-0.01410.14986.10042.42013.4320.0231-0.0055-0.13210.4640.1119-0.14110.82780.5764-0.19640.43490.22830.01240.54190.16150.372421.5148-17.028121.1773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 115 )A-2 - 115
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 149 )A116 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 195 )A150 - 195

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