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- PDB-5vp8: I38T mutant of 2009 H1N1 PA Endonuclease -

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Basic information

Entry
Database: PDB / ID: 5vp8
TitleI38T mutant of 2009 H1N1 PA Endonuclease
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Nuclease Influenza Resistance RO-7 / 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 / 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
Chem-9HD / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKumar, G. / White, S.W.
Funding support United States, Switzerland, 3items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)HHSN272201400006C United States
Roche Innovation Center Switzerland
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: MBio / Year: 2018
Title: Identification of the I38T PA Substitution as a Resistance Marker for Next-Generation Influenza Virus Endonuclease Inhibitors.
Authors: Jones, J.C. / Kumar, G. / Barman, S. / Najera, I. / White, S.W. / Webby, R.J. / Govorkova, E.A.
History
DepositionMay 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8294
Polymers23,1361
Non-polymers6933
Water37821
1
A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules

A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,31616
Polymers92,5454
Non-polymers2,77112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-x+1,-y+3,z1
crystal symmetry operation3_765-y+2,x+1,z1
crystal symmetry operation4_475y-1,-x+2,z1
Buried area6130 Å2
ΔGint-107 kcal/mol
Surface area32880 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-21 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.098, 90.098, 134.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Polymerase acidic protein


Mass: 23136.289 Da / Num. of mol.: 1 / Mutation: I38T, Loop replaced with GGS linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: swl A/California/04/2009 H1N1 / Gene: PA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3W5S0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-9HD / 1-[(3R,5S,7R)-1,5,7,9-tetrakis(2-oxopyrrolidin-1-yl)nonan-3-yl]-1,3-dihydro-2H-pyrrol-2-one / Polyvinylpyrrolidone K15


Mass: 541.682 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H43N5O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES pH 7.8, 1 M Ammonium Sulfate, 10 mM MnCl2, 10 mM MgCl2, 0.5% PVP K15

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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: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14303 / % possible obs: 99.3 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.025 / Rrim(I) all: 0.09 / Χ2: 1.317 / Net I/σ(I): 10.3 / Num. measured all: 178503
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.288.30.91913200.7050.3170.9780.71894.6
2.28-2.3710.90.81714070.8670.2520.8570.73399.2
2.37-2.48130.62713990.9420.1790.6520.75599.8
2.48-2.6113.50.4314160.9740.120.4460.81899.8
2.61-2.7713.50.31614250.9830.0880.3280.89599.9
2.77-2.9913.50.19614290.9930.0550.2041.11799.9
2.99-3.2913.40.12114340.9960.0340.1261.424100
3.29-3.7613.20.08114510.9970.0230.0841.892100
3.76-4.74130.06314640.9980.0180.0652.216100
4.74-5012.20.05515580.9980.0160.0572.19899.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.37 Å46.19 Å
Translation5.37 Å46.19 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
SERGUIdata collection
HKL-2000data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CZN

5czn


Resolution: 2.2→46.19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2443 / WRfactor Rwork: 0.2055 / FOM work R set: 0.773 / SU B: 16.027 / SU ML: 0.179 / SU R Cruickshank DPI: 0.2002 / SU Rfree: 0.1763 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 678 4.7 %RANDOM
Rwork0.2003 ---
obs0.202 13622 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.7 Å2 / Biso mean: 63.374 Å2 / Biso min: 40.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20 Å2
2--1.37 Å20 Å2
3----2.74 Å2
Refinement stepCycle: final / Resolution: 2.2→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 45 21 1509
Biso mean--78.85 57.36 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.021521
X-RAY DIFFRACTIONr_bond_other_d0.0030.021380
X-RAY DIFFRACTIONr_angle_refined_deg2.3671.9592049
X-RAY DIFFRACTIONr_angle_other_deg1.2162.9883203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0745178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41223.33372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67615266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4841511
X-RAY DIFFRACTIONr_chiral_restr0.1210.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021664
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02325
LS refinement shellResolution: 2.199→2.256 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 42 -
Rwork0.331 929 -
all-971 -
obs--93.82 %
Refinement TLS params.Method: refined / Origin x: 38.193 Å / Origin y: 111.177 Å / Origin z: 286.361 Å
111213212223313233
T0.343 Å2-0.0535 Å20.1993 Å2-0.1281 Å20.0425 Å2--0.2323 Å2
L6.0569 °2-0.7966 °21.8357 °2-1.753 °2-0.1649 °2--2.7957 °2
S0.1748 Å °-0.1542 Å °-0.6035 Å °0.2066 Å °-0.3109 Å °0.1195 Å °0.4983 Å °0.0345 Å °0.1361 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 176
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A202
4X-RAY DIFFRACTION1A203

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