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- PDB-6ws3: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 6ws3
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease wild type bound to DNA oligomers TG and AGCA (from cleaved GTGAGCAGTG)
Components
  • DNA (5'-D(P*TP*G)-3')
  • Protein PA-X,Polymerase acidic protein
KeywordsVIRAL PROTEIN/DNA / NUCLEASE / INFLUENZA / DNA oligomer / cleaved / VIRAL PROTEIN / VIRAL PROTEIN-DNA complex / 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
: / DNA / Protein PA-X / Protein PA-X
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCuypers, M.G. / Kumar, G. / Webb, T. / 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
DepositionApr 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,Polymerase acidic protein
F: DNA (5'-D(P*TP*G)-3')
E: DNA (5'-D(P*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8308
Polymers29,3983
Non-polymers4315
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.646, 89.646, 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 / DNA chain , 2 types, 3 molecules AFE

#1: Protein Protein PA-X,Polymerase acidic protein


Mass: 23148.344 Da / Num. of mol.: 1
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) / Strain (production host): BL21(DE3) / References: UniProt: A0A4P2TE19, UniProt: C6H0Y9
#2: DNA chain DNA (5'-D(P*TP*G)-3')


Mass: 3125.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: cleaved by PAN09 between G3 and A4 / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 82 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#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.: 77 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE, 0.02M MGCL2, 0.02M MNCL2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14021 / % possible obs: 99 % / Redundancy: 3.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.042 / Rrim(I) all: 0.104 / Net I/σ(I): 20.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2145 / CC1/2: 0.684 / Rpim(I) all: 0.486 / Rrim(I) all: 0.969 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5vpt

5vpt


Resolution: 2.2→38.4 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.17
RfactorNum. reflection% reflection
Rfree0.2156 752 5.37 %
Rwork0.1902 --
obs0.1916 14011 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 221.2 Å2 / Biso mean: 77.7445 Å2 / Biso min: 37.24 Å2
Refinement stepCycle: final / Resolution: 2.2→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 107 23 77 1634
Biso mean--117.79 77.53 -
Num. residues----185
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 (%)
2.2-2.370.36891270.29432509263695
2.37-2.610.24011470.230426292776100
2.61-2.990.24131700.207726272797100
2.99-3.770.1921350.189227012836100
3.77-38.40.20361730.17072793296699
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)
14.3977-1.18722.32628.0364-2.79038.5813-0.1290.7349-0.0111-1.16980.1050.44630.4366-0.1720.03910.5807-0.04860.00220.6423-0.16260.4304289.6381-34.9863408.9045
23.7128-0.7041-0.92248.9653-0.1441.3416-0.3757-0.40590.04060.16020.37340.17230.0318-0.5923-0.01820.52710.0630.11540.6847-0.08140.3027288.2255-46.1944424.2876
32.06990.5582-0.16276.7253-3.80736.4764-0.304-0.10830.06250.57260.1859-0.0144-0.5461-0.57290.01360.38310.14860.01890.5357-0.22080.3652291.1389-30.2004423.7004
40.0926-0.57150.11473.7779-0.73840.1450.5191-0.179-0.9449-1.1775-0.8661-1.3937-1.9096-1.6770.24412.22260.0264-0.6531.77980.75463.1197277.0953-48.4579415.9185
57.62894.7992-1.58593.9105-2.13811.78941.1971.64630.6277-0.28941.2420.22290.6254-1.0134-1.63241.59850.6718-0.15873.2848-0.84881.7112279.9952-33.5968417.9412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 51 )A-2 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 118 )A52 - 118
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 175 )A119 - 175
4X-RAY DIFFRACTION4chain 'F' and (resid 1 through 2 )F1 - 2
5X-RAY DIFFRACTION5chain 'E' and (resid 3 through 6 )E3 - 6

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