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

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Basic information

Entry
Database: PDB / ID: 8djy
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 viral polymerase in complex with 6-Bromo-2-(4,5-dihydro-1H-imidazol-2-yl)-3-hydroxypyridin-4(1H)-one
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / HYDROLASE/INHIBITOR / Drug discovery / metal-binding pharmacophore / isosteres / influenza endonuclease / VIRAL PROTEIN-INHIBITOR complex / 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-U3L / Polymerase PA
Function and homology information
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

Downloads & links

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7924
Polymers22,4251
Non-polymers3683
Water1,36976
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)75.807, 75.807, 119.978
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-317-

HOH

21A-337-

HOH

31A-365-

HOH

41A-371-

HOH

51A-372-

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-U3L / (2M)-6-bromo-2-(4,5-dihydro-1H-imidazol-2-yl)-3-hydroxypyridin-4(1H)-one


Mass: 258.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8BrN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
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: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→44.29 Å / Num. obs: 13372 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 51.67 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.093 / Net I/σ(I): 20
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 1.243 / Mean I/σ(I) obs: 2 / Num. unique obs: 732 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6V

6e6v


Resolution: 2.5→44.29 Å / SU ML: 0.4031 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7712
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.286 1353 10.12 %
Rwork0.2116 12019 -
obs0.2192 13372 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.49 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 16 76 1559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081515
X-RAY DIFFRACTIONf_angle_d0.86392035
X-RAY DIFFRACTIONf_chiral_restr0.0534217
X-RAY DIFFRACTIONf_plane_restr0.0081259
X-RAY DIFFRACTIONf_dihedral_angle_d18.8882566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.39641360.33581204X-RAY DIFFRACTION99.48
2.59-2.690.35731350.29141206X-RAY DIFFRACTION100
2.69-2.810.3211380.29471192X-RAY DIFFRACTION100
2.82-2.960.34011350.2761202X-RAY DIFFRACTION99.93
2.96-3.150.39791320.28511208X-RAY DIFFRACTION100
3.15-3.390.34721300.25111194X-RAY DIFFRACTION99.92
3.39-3.730.30661370.19261204X-RAY DIFFRACTION100
3.73-4.270.30031350.16761201X-RAY DIFFRACTION99.93
4.27-5.380.20491370.1631198X-RAY DIFFRACTION100
5.39-44.290.22661380.19071210X-RAY DIFFRACTION100
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)
12.010214921377.84696588911.969801570518.30585760024-1.951174012866.0066779242-0.09852863964980.945161579082-0.574385440078-0.6650158843160.1762316768170.3211344089780.1992920151290.325178180179-0.06472636705750.6422609926560.1303588019460.07627594304940.491677309019-0.1038625781030.49981343811729.92970823737.60031309907-20.136696249
28.625179254450.61875701451-1.999515465590.4977444997780.1369323896491.703795403180.126762618208-0.0929945058709-0.2228665084160.100920307147-0.09645995233810.206536549769-0.0432067641759-0.051075545837-0.01174704312420.5786685993820.01569767700310.1072733190180.244766098873-0.007162576927430.38948884903215.266245096712.8685982308-8.12206970654
39.2901818606-1.47284247788-1.621455886060.903059171746-0.3554406629222.326172248750.1678245754740.1486961039490.3787256226190.0700365841344-0.1182474682570.115394204005-0.189443348494-0.0564512907773-0.02601600263040.534747469901-0.03026651736010.02213979548240.185087393148-0.02626951026950.35609627064627.536956329819.833518114-5.42916499146
Refinement TLS group

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

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 31 )-1 - 312 - 34
22chain 'A' and (resid 32 through 126 )32 - 12635 - 109
33chain 'A' and (resid 127 through 198 )127 - 198110 - 181

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