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- PDB-5vrj: 2009 H1N1 PA Endonuclease in complex with RO-7 and Magnesium -

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Basic information

Entry
Database: PDB / ID: 5vrj
Title2009 H1N1 PA Endonuclease in complex with RO-7 and Magnesium
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Nuclease Influenza Inhibitor Resistance / 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 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-R07 / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.302 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 10, 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 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)23,7815
Polymers23,1481
Non-polymers6324
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Protein elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-26 kcal/mol
Surface area9260 Å2
2
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)95,12220
Polymers92,5934
Non-polymers2,52916
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-130 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.924, 90.924, 133.913
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: 23148.344 Da / Num. of mol.: 1 / Mutation: 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-R07 / 1-[(11S)-6,11-dihydrodibenzo[b,e]thiepin-11-yl]-5-hydroxy-3-[(2R)-1,1,1-trifluoropropan-2-yl]-2,3-dihydro-1H-pyrido[2,1-f][1,2,4]triazine-4,6-dione / RO-7


Mass: 487.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20F3N3O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M HEPES pH 7.8, 1 M Ammonium Sulfate, 50 mM MgCl2, 1% 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: 2.3→50 Å / Num. obs: 12688 / % possible obs: 99 % / Redundancy: 7.9 % / Biso Wilson estimate: 56.55 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.03 / Rrim(I) all: 0.087 / Χ2: 1.158 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.384.70.8430.7490.3760.9310.7591.3
2.38-2.486.10.8470.810.340.9170.77499.2
2.48-2.597.60.7560.8790.2840.810.796100
2.59-2.738.70.6440.9360.230.6850.802100
2.73-2.98.90.4020.9730.1430.4270.897100
2.9-3.128.80.2390.9860.0850.2541.207100
3.12-3.448.80.1350.9940.0480.1431.313100
3.44-3.938.80.0710.9980.0250.0751.478100
3.93-4.958.60.0510.9980.0180.0551.574100
4.95-5080.0430.9990.0160.0461.55599.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.39 Å38.91 Å
Translation5.39 Å38.91 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data processing
SERGUIdata collection
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.302→38.908 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.12
RfactorNum. reflection% reflection
Rfree0.2471 686 5.41 %
Rwork0.1994 --
obs0.2021 12678 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.12 Å2 / Biso mean: 75.8635 Å2 / Biso min: 45.8 Å2
Refinement stepCycle: final / Resolution: 2.302→38.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 41 3 1482
Biso mean--72.52 63.39 -
Num. residues----179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081511
X-RAY DIFFRACTIONf_angle_d1.0512042
X-RAY DIFFRACTIONf_chiral_restr0.067214
X-RAY DIFFRACTIONf_plane_restr0.006259
X-RAY DIFFRACTIONf_dihedral_angle_d3.82887
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3024-2.48020.33931340.27382242237695
2.4802-2.72970.29361440.234423662510100
2.7297-3.12450.31631260.228124072533100
3.1245-3.9360.2241300.196324232553100
3.936-38.91380.22981520.182625542706100
Refinement TLS params.Method: refined / Origin x: 38.465 Å / Origin y: 112.133 Å / Origin z: 286.072 Å
111213212223313233
T0.7571 Å2-0.0975 Å20.248 Å2-0.3783 Å20.066 Å2--0.5201 Å2
L6.2295 °2-0.1664 °21.4799 °2-1.6074 °2-0.2584 °2--3.1722 °2
S0.2075 Å °-0.2733 Å °-0.276 Å °0.1469 Å °-0.3777 Å °0.0171 Å °0.7753 Å °-0.1373 Å °0.1469 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:203 OR RESID 301:303 OR RESID 204:204 ) )A-2 - 176
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:203 OR RESID 301:303 OR RESID 204:204 ) )A201
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:203 OR RESID 301:303 OR RESID 204:204 ) )A202 - 203
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:203 OR RESID 301:303 OR RESID 204:204 ) )A301 - 303
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:203 OR RESID 301:303 OR RESID 204:204 ) )A204

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