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- PDB-5vpt: 2009 H1N1 PA Endonuclease in complex with RO-7 -

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Basic information

Entry
Database: PDB / ID: 5vpt
Title2009 H1N1 PA Endonuclease in complex with RO-7
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 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 / Resolution: 2.1 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 5, 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_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

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8425
Polymers23,1481
Non-polymers6934
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-22 kcal/mol
Surface area9270 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)95,36720
Polymers92,5934
Non-polymers2,77416
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 area6210 Å2
ΔGint-111 kcal/mol
Surface area32230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.881, 89.881, 133.731
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / 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-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.: 25 / 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: 2.92 Å3/Da / Density % sol: 57.83 %
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: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.091→38.495 Å / Num. obs: 16185 / % possible obs: 97.49 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.017 / Rrim(I) all: 0.05 / Χ2: 0.946 / Net I/σ(I): 10.9 / Num. measured all: 127165
Reflection shellResolution: 2.091→2.166 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.602 / Num. unique obs: 1321 / CC1/2: 0.848 / Rpim(I) all: 0.256 / Rrim(I) all: 0.658 / Χ2: 0.764 / % possible all: 82.04

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Processing

Software
NameVersionClassification
SERGUIdata collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXrefinement
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VP8

5vp8


Resolution: 2.1→38.495 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7
RfactorNum. reflection% reflection
Rfree0.2203 854 5.28 %
Rwork0.2 --
obs0.2012 16185 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.85 Å2 / Biso mean: 67.9741 Å2 / Biso min: 38.82 Å2
Refinement stepCycle: final / Resolution: 2.1→38.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1440 0 41 25 1506
Biso mean--60.44 62.51 -
Num. residues----179
Refinement TLS params.Method: refined / Origin x: 38.084 Å / Origin y: 110.513 Å / Origin z: 285.726 Å
111213212223313233
T0.6681 Å2-0.1188 Å20.2087 Å2-0.3178 Å20.0634 Å2--0.4319 Å2
L5.7972 °2-0.507 °20.6365 °2-2.4176 °2-0.1505 °2--2.9898 °2
S0.1848 Å °-0.2168 Å °-0.2637 Å °0.0961 Å °-0.3023 Å °0.0896 Å °0.6792 Å °-0.1222 Å °0.0498 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 202:202 OR RESID 203:203 OR RESID 204:204 ) )A-2 - 176
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:202 OR RESID 203:203 OR RESID 204:204 ) )A201
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:202 OR RESID 203:203 OR RESID 204:204 ) )A202
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:202 OR RESID 203:203 OR RESID 204:204 ) )A203
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID -2:176 OR RESID 201:201 OR RESID 202:202 OR RESID 203:203 OR RESID 204:204 ) )A204

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