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- PDB-5d9j: 2009 H1N1 PA endonuclease mutant F105S in complex with L-742,001 -

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Basic information

Entry
Database: PDB / ID: 5d9j
Title2009 H1N1 PA endonuclease mutant F105S in complex with L-742,001
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / influenza / resistance / endonuclease inhibitor / viral protein / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-0N8 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKumar, G. / White, S.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI098757 United States
St. Jude Children's Research Hospital (ALSAC) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Identification and characterization of influenza variants resistant to a viral endonuclease inhibitor.
Authors: Song, M.S. / Kumar, G. / Shadrick, W.R. / Zhou, W. / Jeevan, T. / Li, Z. / Slavish, P.J. / Fabrizio, T.P. / Yoon, S.W. / Webb, T.R. / Webby, R.J. / White, S.W.
History
DepositionAug 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)22,4344
Polymers21,9101
Non-polymers5243
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-7 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.585, 60.585, 95.980
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Polymerase acidic protein / PA endonuclease


Mass: 21910.064 Da / Num. of mol.: 1
Fragment: endonuclease domain (UNP residues 1-50, 73-196 connected by GGS linker)
Mutation: F105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: PA / Plasmid: pET52b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3W5S0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-0N8 / (2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid


Mass: 413.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClNO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.8 M succinic acid, pH 7.0, 5 mM magnesium chloride, 5 mM manganese chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 9, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 17865 / % possible obs: 100 % / Redundancy: 18.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.015 / Rrim(I) all: 0.065 / Χ2: 0.92 / Net I/av σ(I): 43.273 / Net I/σ(I): 10.3 / Num. measured all: 335403
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.9215.70.88317640.8890.2260.9120.686100
1.92-1.9918.80.62217420.9530.1460.6390.735100
1.99-2.0819.40.40217680.9810.0930.4130.786100
2.08-2.1919.40.26217410.9910.0610.2690.864100
2.19-2.3319.50.18317780.9950.0420.1880.947100
2.33-2.5119.40.1317710.9970.030.1331.025100
2.51-2.7619.40.09317850.9990.0220.0950.997100
2.76-3.1619.30.06817850.9990.0160.071.026100
3.16-3.9819.10.04818060.9990.0110.050.992100
3.98-4017.90.03819250.9990.0090.0391.08699.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E5E

4e5e


Resolution: 1.85→35.41 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.202 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 960 5.4 %RANDOM
Rwork0.1826 ---
obs0.1851 16871 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.22 Å2 / Biso mean: 42.079 Å2 / Biso min: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.85→35.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 24 64 1501
Biso mean--40.21 42.85 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0191464
X-RAY DIFFRACTIONr_bond_other_d0.0040.021344
X-RAY DIFFRACTIONr_angle_refined_deg2.6151.961975
X-RAY DIFFRACTIONr_angle_other_deg1.28833080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53222.68767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55415250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8921513
X-RAY DIFFRACTIONr_chiral_restr0.170.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021642
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02349
X-RAY DIFFRACTIONr_mcbond_it2.3622.612715
X-RAY DIFFRACTIONr_mcbond_other2.3592.608714
X-RAY DIFFRACTIONr_mcangle_it3.2983.899892
LS refinement shellResolution: 1.854→1.902 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 63 -
Rwork0.249 1231 -
all-1294 -
obs--98.33 %
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)
10.7611-0.0412-0.4251.99080.44880.8854-0.1864-0.1005-0.0294-0.01140.2957-0.00490.00950.1374-0.10930.2505-0.10180.01720.13220.00490.028982.76588.36150.5986
212.1493-0.3279-7.51861.4557-0.86285.48520.2082-0.57580.08390.0245-0.06790.1961-0.17430.4619-0.14020.097-0.0383-0.02630.0850.03110.103184.568888.09538.4652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION2C1

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