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- PDB-5ccy: 2009 H1N1 PA endonuclease in complex with dTMP -

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Basic information

Entry
Database: PDB / ID: 5ccy
Title2009 H1N1 PA endonuclease in complex with dTMP
ComponentsPolymerase acidic protein
KeywordsHYDROLASE / influenza / resistance / endonuclease / inhibitor
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: 2.1 Å
AuthorsKumar, G. / White, S.W.
Funding support United States, 3items
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
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
DepositionJul 2, 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 6, 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 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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)22,4024
Polymers21,9701
Non-polymers4323
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-16 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.908, 73.908, 128.282
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


Mass: 21970.160 Da / Num. of mol.: 1 / Fragment: endonuclease domain (UNP residues 1-50, 73-196)
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.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 % / Description: Hexagonal plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M magnesium chloride, 5 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-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2014
RadiationMonochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→64.006 Å / Num. obs: 12747 / % possible obs: 100 % / Redundancy: 28.4 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.022 / Rrim(I) all: 0.121 / Χ2: 0.868 / Net I/av σ(I): 33.308 / Net I/σ(I): 6 / Num. measured all: 361856
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1828.10.96512430.920.1790.9820.816100
2.18-2.2628.50.74212130.9570.1370.7550.811100
2.26-2.3728.30.58312480.9750.1080.5930.812100
2.37-2.4928.40.46712370.9830.0870.4760.822100
2.49-2.6528.60.30812620.9920.0570.3130.829100
2.65-2.8528.60.22312630.9960.0410.2270.845100
2.85-3.14290.14712530.9980.0270.150.926100
3.14-3.5929.30.11212820.9980.0210.1141.055100
3.59-4.5228.90.072131010.0140.0730.904100
4.52-5026.40.036143610.0070.0360.84499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E5E

4e5e


Resolution: 2.1→50.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.978 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2438 623 4.9 %RANDOM
Rwork0.1712 ---
obs0.1747 12084 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.51 Å2 / Biso mean: 37.181 Å2 / Biso min: 18.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.23 Å20 Å2
2---0.47 Å20 Å2
3---1.51 Å2
Refinement stepCycle: final / Resolution: 2.1→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 23 88 1569
Biso mean--34.54 39.9 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191510
X-RAY DIFFRACTIONr_bond_other_d0.0030.021409
X-RAY DIFFRACTIONr_angle_refined_deg2.1981.9572033
X-RAY DIFFRACTIONr_angle_other_deg1.19433240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49523.02676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91415275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0321514
X-RAY DIFFRACTIONr_chiral_restr0.1620.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021672
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02364
X-RAY DIFFRACTIONr_mcbond_it2.2212.748711
X-RAY DIFFRACTIONr_mcbond_other2.2162.746710
X-RAY DIFFRACTIONr_mcangle_it3.2954.105887
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 49 -
Rwork0.184 847 -
all-896 -
obs--98.46 %
Refinement TLS params.Method: refined / Origin x: -14.2484 Å / Origin y: 75.4169 Å / Origin z: 14.1762 Å
111213212223313233
T0.0906 Å20.0021 Å20.0418 Å2-0.0221 Å2-0.0217 Å2--0.0528 Å2
L0.149 °2-0.1455 °2-0.1227 °2-0.98 °20.4831 °2--1.4334 °2
S-0.0646 Å °-0.0017 Å °-0.0501 Å °-0.0003 Å °-0.0586 Å °0.0465 Å °0.1418 Å °-0.0208 Å °0.1232 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 178
2X-RAY DIFFRACTION1A201 - 203

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