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- PDB-6w7a: The crystal structure of the 2009/H1N1/California PA endonuclease... -

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Basic information

Entry
Database: PDB / ID: 6w7a
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease mutant E119D bound to DNA oligomer TAGCAT (uncleaved, 5mM overnight DNA soak)
Components
  • DNA (5'-D(P*TP*AP*GP*CP*AP*T)-3')
  • Protein PA-X,Polymerase acidic protein
KeywordsVIRAL PROTEIN/DNA / NUCLEASE / INFLUENZA / DNA oligomer / uncleaved / VIRAL PROTEIN / VIRAL PROTEIN-DNA complex
Function / homology
Function and homology information


viral translational frameshifting / 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 / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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
DepositionMar 18, 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 1.2Jun 21, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 25, 2023Group: 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: Protein PA-X,Polymerase acidic protein
B: DNA (5'-D(P*TP*AP*GP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8866
Polymers25,5512
Non-polymers3354
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-31 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.301, 89.301, 134.024
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, 2 molecules AB

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


Mass: 23134.316 Da / Num. of mol.: 1 / Mutation: E119D
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 / Variant: H1N1/California/2009 / Strain: A/Luxembourg/43/2009(H1N1) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4P2TE19, UniProt: C6H0Y9
#2: DNA chain DNA (5'-D(P*TP*AP*GP*CP*AP*T)-3')


Mass: 2416.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ssDNA / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 115 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.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES PH 7.8, 1 M AMMONIUM SULFATE / Temp details: controlled temperature room

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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: Mar 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 16288 / % possible obs: 98.9 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.108 / Net I/σ(I): 25
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1435 / CC1/2: 0.865 / Rpim(I) all: 0.219 / Rrim(I) all: 0.594 / % possible all: 89.6

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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: 2.09→39.95 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.9
Details: refmac5 then rigid body with phenix.refine for final check
RfactorNum. reflection% reflection
Rfree0.2049 818 5.03 %
Rwork0.1744 --
obs0.176 16274 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.35 Å2 / Biso mean: 57.9536 Å2 / Biso min: 28.14 Å2
Refinement stepCycle: final / Resolution: 2.09→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 123 18 111 1691
Biso mean--86.79 62.27 -
Num. residues----184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.220.30361150.2382370248593
2.22-2.390.23771140.195525842698100
2.39-2.630.2281450.182625802725100
2.63-3.010.20351330.18825782711100
3.01-3.790.19661540.167825992753100
3.79-39.950.19161570.160827452902100
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)
14.15011.08082.07772.80611.67066.49160.09080.725-0.1276-0.2655-0.047-0.01970.67590.6158-0.10680.62930.00810.09640.55250.0030.2569124.0053199.2047275.7782
26.24920.7581-0.08911.9732-0.89611.43060.1418-0.2015-0.12090.0735-0.2073-0.13390.40920.15090.05870.5464-0.02450.07140.3980.0340.1925135.1559197.7374291.1521
34.1951-0.83052.68061.0821-1.50085.8430.2128-0.28610.1448-0.1228-0.19190.06150.4683-0.5412-0.2410.4644-0.11470.11950.3570.00350.1797119.2384200.7041290.5035
45.20423.19974.23535.78773.70523.76410.2580.2521-1.8996-0.8456-0.0241-0.68692.160.16110.89161.2018-0.17230.07750.63330.08080.7121122.6735186.8869284.6415
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 'B' and (resid 0 through 5 )B0 - 5

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