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- PDB-5cl0: 2009 H1N1 PA endonuclease in complex with rUMP -

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Basic information

Entry
Database: PDB / ID: 5cl0
Title2009 H1N1 PA endonuclease in complex with rUMP
ComponentsPolymerase acidic protein
KeywordsVIRAL PROTEIN / influenza / resistance / endonuclease inhibitor
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
: / URIDINE-5'-MONOPHOSPHATE / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 15, 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 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 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)22,4044
Polymers21,9701
Non-polymers4343
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-18 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.946, 73.946, 128.584
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


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-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
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: 2.22→50 Å / Num. obs: 10855 / % possible obs: 99.8 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.027 / Rrim(I) all: 0.094 / Χ2: 1.216 / Net I/av σ(I): 31.943 / Net I/σ(I): 8.3 / Num. measured all: 153418
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.22-2.3140.98110530.8750.2641.14799.9
2.3-2.3914.50.75810510.9010.2021.1421000.785
2.39-2.514.50.56310420.9440.151.1441000.583
2.5-2.6314.50.39510690.9730.1061.1881000.409
2.63-2.814.40.28110590.9850.0751.1721000.291
2.8-3.0114.40.18310700.9940.0491.2151000.19
3.01-3.3214.30.11710790.9970.0311.2181000.121
3.32-3.814.10.06810960.9990.0181.3861000.071
3.8-4.7813.90.05811240.9990.0161.3199.90.06
4.78-5012.80.035121210.011.22898.70.037

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Processing

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

5ccy


Resolution: 2.22→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.028 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 522 4.8 %RANDOM
Rwork0.1915 ---
obs0.1938 10308 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.08 Å2 / Biso mean: 44.192 Å2 / Biso min: 24.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---2.14 Å2
Refinement stepCycle: final / Resolution: 2.22→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 23 61 1542
Biso mean--57.11 44.03 -
Num. residues----178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191510
X-RAY DIFFRACTIONr_bond_other_d0.0020.021406
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9572033
X-RAY DIFFRACTIONr_angle_other_deg0.95633234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7425177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40623.02676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25615275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9681514
X-RAY DIFFRACTIONr_chiral_restr0.090.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021671
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02365
X-RAY DIFFRACTIONr_mcbond_it1.6533.516711
X-RAY DIFFRACTIONr_mcbond_other1.6513.514710
X-RAY DIFFRACTIONr_mcangle_it2.7265.267887
LS refinement shellResolution: 2.222→2.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 44 -
Rwork0.249 724 -
all-768 -
obs--99.61 %
Refinement TLS params.Method: refined / Origin x: -14.2157 Å / Origin y: 75.4937 Å / Origin z: 14.2503 Å
111213212223313233
T0.0997 Å20.0004 Å20.0377 Å2-0.0235 Å2-0.0165 Å2--0.0568 Å2
L0.1477 °2-0.1542 °2-0.056 °2-0.9489 °20.4239 °2--1.3118 °2
S-0.0529 Å °0.0051 Å °-0.0664 Å °-0.0059 Å °-0.0461 Å °0.0232 Å °0.1068 Å °-0.0004 Å °0.099 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 178
2X-RAY DIFFRACTION1C301

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