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- PDB-5d42: 2009 H1N1 PA endonuclease mutant F105S in complex with dTMP -

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Basic information

Entry
Database: PDB / ID: 5d42
Title2009 H1N1 PA endonuclease mutant F105S in complex with dTMP
ComponentsPolymerase acidic protein
KeywordsHYDROLASE / influenza / resistance / endonuclease inhibitor / viral protein
Function / homology
Function and homology information


symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / 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
: / THYMIDINE-5'-PHOSPHATE / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 7, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)22,3424
Polymers21,9101
Non-polymers4323
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-17 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.084, 74.084, 130.312
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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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, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Water ChemComp-HOH / water / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 2 mM manganese chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000

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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 4, 2015
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: 2→50 Å / Num. obs: 14714 / % possible obs: 98.7 % / Redundancy: 14 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.018 / Rrim(I) all: 0.069 / Χ2: 1.126 / Net I/av σ(I): 37.053 / Net I/σ(I): 11.8 / Num. measured all: 205273
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0711.60.89313300.7590.2550.9310.892.1
2.07-2.1513.10.62213980.8640.1740.6470.86797.8
2.15-2.25140.4514580.930.1250.4690.923100
2.25-2.3714.60.3414650.9690.0940.3530.955100
2.37-2.5214.80.23414530.9870.0640.2431.055100
2.52-2.7114.70.15114730.9940.0410.1571.191100
2.71-2.9914.70.09814860.9970.0260.1011.322100
2.99-3.4214.50.06514940.9990.0170.0671.293100
3.42-4.3114.30.0515300.9990.0130.0511.299100
4.31-5013.10.03616270.9990.010.0381.40297.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5D2O

5d2o


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 9.097 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 761 5.2 %RANDOM
Rwork0.1824 ---
obs0.1852 13931 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.15 Å2 / Biso mean: 47.191 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0.46 Å20 Å2
2---0.91 Å20 Å2
3---2.95 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 23 64 1525
Biso mean--51.08 51.12 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191493
X-RAY DIFFRACTIONr_bond_other_d0.0020.021384
X-RAY DIFFRACTIONr_angle_refined_deg2.2181.9562013
X-RAY DIFFRACTIONr_angle_other_deg1.16333177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03222.97374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75315266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7871514
X-RAY DIFFRACTIONr_chiral_restr0.1250.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021661
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
X-RAY DIFFRACTIONr_mcbond_it2.8013.462711
X-RAY DIFFRACTIONr_mcbond_other2.7983.46710
X-RAY DIFFRACTIONr_mcangle_it3.8735.173887
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 52 -
Rwork0.261 864 -
all-916 -
obs--86.17 %
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)
10.6381-0.6027-0.00950.90730.61611.978-0.0967-0.00290.00560.0234-0.08370.138-0.0762-0.13810.18040.05910.0382-0.01720.0831-0.05710.094621.135313.91897.32
210.2463-5.6704-3.09524.02395.0213.3035-0.04920.4958-0.17840.0124-0.04760.1106-0.08190.67810.09680.0475-0.0183-0.00110.09350.01710.067228.934915.91426.5005
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 179
2X-RAY DIFFRACTION2C1

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