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- PDB-8djv: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -

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Basic information

Entry
Database: PDB / ID: 8djv
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 6-Bromo-3-hydroxy-N-methoxy-4-oxo-1,4-dihydropyridine-2-carboxamide
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / Drug discovery / metal-binding pharmacophore / isosteres / influenza endonuclease / VIRAL PROTEIN-INHIBITOR complex / ANTIVIRAL PROTEIN / HYDROLASE-INHIBITOR complex
Function / homologyInfluenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / viral translational frameshifting / viral RNA genome replication / RNA binding / : / Chem-U3U / Polymerase PA
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsKohlbrand, A.J. / Stokes, R.W. / Karges, J. / Seo, H. / Sankaran, B. / Cohen, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI149444 United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Carboxylic Acid Isostere Derivatives of Hydroxypyridinones as Core Scaffolds for Influenza Endonuclease Inhibitors.
Authors: Stokes, R.W. / Kohlbrand, A.J. / Seo, H. / Sankaran, B. / Karges, J. / Cohen, S.M.
History
DepositionJul 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 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

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7974
Polymers22,4251
Non-polymers3733
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.465, 74.465, 120.259
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

21A-454-

HOH

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Components

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


Mass: 22424.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/California/04/2009(H1N1) / Gene: PA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: C6Y817
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-U3U / 6-bromo-3-hydroxy-N-methoxy-4-oxo-1,4-dihydropyridine-2-carboxamide


Mass: 263.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7BrN2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Aug 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.08→37.24 Å / Num. obs: 22176 / % possible obs: 99.1 % / Redundancy: 17.7 % / Biso Wilson estimate: 37.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.023 / Rrim(I) all: 0.103 / Net I/σ(I): 13
Reflection shellResolution: 2.08→2.15 Å / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1077 / CC1/2: 0.723 / Rrim(I) all: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
APEX 2data reduction
APEX 2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6V

6e6v


Resolution: 2.08→37.23 Å / SU ML: 0.3637 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8966
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.291 2222 10.02 %
Rwork0.2626 19954 -
obs0.2654 22176 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.51 Å2
Refinement stepCycle: LAST / Resolution: 2.08→37.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 16 60 1557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00991528
X-RAY DIFFRACTIONf_angle_d1.20782051
X-RAY DIFFRACTIONf_chiral_restr0.0633217
X-RAY DIFFRACTIONf_plane_restr0.0095262
X-RAY DIFFRACTIONf_dihedral_angle_d19.4713577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.130.39781170.34951056X-RAY DIFFRACTION84.27
2.13-2.170.35381430.3541258X-RAY DIFFRACTION100
2.17-2.230.3431380.34041243X-RAY DIFFRACTION100
2.23-2.290.36581420.3231264X-RAY DIFFRACTION100
2.29-2.360.38481470.3421265X-RAY DIFFRACTION100
2.36-2.430.40771400.36151256X-RAY DIFFRACTION100
2.43-2.520.39281410.33151256X-RAY DIFFRACTION99.86
2.52-2.620.36451450.36111264X-RAY DIFFRACTION100
2.62-2.740.38791400.331249X-RAY DIFFRACTION99.93
2.74-2.880.35891450.33011262X-RAY DIFFRACTION100
2.88-3.070.32641370.30351258X-RAY DIFFRACTION100
3.07-3.30.32151370.29421256X-RAY DIFFRACTION99.71
3.3-3.630.27981420.25071261X-RAY DIFFRACTION100
3.63-4.160.23411390.20381268X-RAY DIFFRACTION99.86
4.16-5.230.21821310.1951266X-RAY DIFFRACTION99.93
5.24-37.230.22711380.21131272X-RAY DIFFRACTION99.93
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)
11.487629943821.991841574150.7224925675333.06168227481-0.4981323922955.71871003042-0.08452293892690.124343407615-0.103136364759-0.0981698317308-0.1037938883160.2636998970950.199642449620.01343489549670.1640199118310.5060540125990.1676868541330.07498279774430.564324989698-0.1596045067930.50616914956529.51162275157.09332174469-20.4139867653
24.78266870026-0.0416449924959-0.5945788489541.516527206150.6592023607122.261795544520.084084743788-0.439190847097-0.3578842857740.0942883188977-0.3337661545590.5278203168030.0990447343068-0.5074912266960.2271845221840.3042368709870.05586146006320.1055026411520.481123221311-0.08305405815470.4251849130714.844012117212.3551324658-8.37125826433
33.38449972975-0.1919038718960.5050416787253.35666517574-0.1273100106523.53307786220.165984388705-0.23574029490.4048230677060.0322585832509-0.2109240925910.179563012832-0.195908110799-0.1310468493990.04202798527590.2237641982210.04490441141440.06123094591820.371247926527-0.0322956622230.34986159741927.147712749819.2622410959-5.64143597868
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 31 )-1 - 311 - 33
22chain 'A' and (resid 32 through 126 )32 - 12634 - 108
33chain 'A' and (resid 127 through 198 )127 - 198109 - 180

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