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

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Basic information

Entry
Database: PDB / ID: 6whm
TitleThe crystal structure of the 2009/H1N1/California PA endonuclease wild type bound to DNA oligomer TAGC (cleaved TTAGCATT, 5mM overnight DNA soak)
Components
  • DNA (5'-D(P*TP*AP*GP*C)-3')
  • PA-X protein,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: 1.92 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 8, 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

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Assembly

Deposited unit
A: PA-X protein,Polymerase acidic protein
B: DNA (5'-D(P*TP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0459
Polymers25,5652
Non-polymers4807
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-56 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.885, 89.885, 134.295
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein PA-X protein,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))
Cell line: 2009/H1N1/CALIFORNIA / Gene: PA-X, PA / Variant: 2009/H1N1/CALIFORNIA / Strain: A/Luxembourg/43/2009(H1N1) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A481PFF5, UniProt: C6H0Y9
#2: DNA chain DNA (5'-D(P*TP*AP*GP*C)-3')


Mass: 2416.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 5 types, 143 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.63 %
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.
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: Aug 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 21245 / % possible obs: 99.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 39.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Net I/σ(I): 46.4
Reflection shellResolution: 1.92→1.99 Å / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2 / Num. unique obs: 2048 / CC1/2: 0.786 / Rpim(I) all: 0.308 / Rrim(I) all: 0.74 / % possible all: 95.5

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Processing

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

5vpt


Resolution: 1.92→37.35 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 983 4.63 %
Rwork0.1772 20252 -
obs0.179 21235 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.86 Å2 / Biso mean: 59.2088 Å2 / Biso min: 28.91 Å2
Refinement stepCycle: final / Resolution: 1.92→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 82 25 136 1673
Biso mean--109.99 64.67 -
Num. residues----183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-2.020.29981310.25792791292298
2.02-2.150.22321290.206728873016100
2.15-2.320.25541320.18628582990100
2.32-2.550.21751560.185528523008100
2.55-2.920.20611580.187928803038100
2.92-3.680.25051200.179329493069100
3.68-37.350.19561570.16173035319299
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)
16.32711.66474.92642.2291.30377.90820.11330.7544-0.2214-0.1516-0.04540.01490.51650.4621-0.07980.4744-0.03210.17830.397-0.00690.3925125.0336200.9506276.5012
28.31430.23120.55222.9199-0.69572.27430.3279-0.03420.16910.1055-0.3205-0.08020.27320.13160.00450.4346-0.02120.1130.32560.09190.3271138.1961201.024290.5245
38.84245.10221.30334.4339-1.54766.460.5369-0.3625-1.0489-0.0088-0.398-0.26861.0655-0.0473-0.14510.6937-0.15380.12620.40710.09960.4943127.3521193.6817296.3051
45.0088-0.59683.14480.80280.39036.94390.123-0.4052-0.130.0284-0.16080.10590.5613-0.72960.01410.4162-0.13510.18480.3374-0.00420.3979117.5274203.6061289.7197
50.5660.28470.59074.7036-5.40987.7573-0.9354-0.5079-3.4639-2.8905-0.1671-2.17912.74360.51161.34111.7786-0.32180.80311.0780.40442.1463122.4721189.5782285.6444
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 107 )A52 - 107
3X-RAY DIFFRACTION3chain 'A' and (resid 108 through 130 )A108 - 130
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 175 )A131 - 175
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 4 )B1 - 4

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