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- PDB-5cgv: 2009 H1N1 PA endonuclease in complex with L-742,001 -

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Basic information

Entry
Database: PDB / ID: 5cgv
Title2009 H1N1 PA endonuclease in complex with L-742,001
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Influenza Resistance Endonuclease Inhibitor / 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 / 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
Chem-0N8 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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. U.S.A. / 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 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 1.2May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 / 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)22,5865
Polymers21,9701
Non-polymers6164
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.899, 73.899, 127.457
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: residues 1-196
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 (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-0N8 / (2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid


Mass: 413.894 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClNO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2, 5mM MnCl2, 0.1 M Tris pH 8.5, 30%(w/v) PEG 4000

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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: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 11511 / % possible obs: 99.8 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.037 / Rrim(I) all: 0.133 / Χ2: 1.285 / Net I/av σ(I): 22.4 / Net I/σ(I): 6.6 / Num. measured all: 146974
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.17-2.258.10.89310900.7630.3190.9521.23498.3
2.25-2.3411.40.79911030.9240.2440.8371.239100
2.34-2.4413.80.69211310.9150.1930.7191.271100
2.44-2.5713.80.51511230.9530.1430.5351.291100
2.57-2.7313.80.3711290.9720.1030.3841.301100
2.73-2.9513.80.24811360.9880.0690.2581.29100
2.95-3.2413.70.15711450.9950.0440.1631.317100
3.24-3.7113.60.08311670.9990.0230.0861.315100
3.71-4.6713.30.06811850.9980.0190.071.254100
4.67-5012.10.04813020.9990.0140.051.30599.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E5E

4e5e


Resolution: 2.17→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.905 / SU B: 18.445 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28166 549 4.8 %RANDOM
Rwork0.19872 ---
obs0.20242 10926 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å2-0.44 Å20 Å2
2---0.87 Å20 Å2
3---2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.17→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 37 64 1553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191518
X-RAY DIFFRACTIONr_bond_other_d0.0020.021409
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.9652042
X-RAY DIFFRACTIONr_angle_other_deg1.20733240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6585177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65223.28976
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.05215270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3071513
X-RAY DIFFRACTIONr_chiral_restr0.1320.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021689
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02368
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1513.158711
X-RAY DIFFRACTIONr_mcbond_other2.1453.156710
X-RAY DIFFRACTIONr_mcangle_it3.4424.732887
X-RAY DIFFRACTIONr_mcangle_other3.4424.735888
X-RAY DIFFRACTIONr_scbond_it2.7723.491807
X-RAY DIFFRACTIONr_scbond_other2.7653.492807
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4945.0951156
X-RAY DIFFRACTIONr_long_range_B_refined6.66825.6751788
X-RAY DIFFRACTIONr_long_range_B_other6.62725.6611778
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.169→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 38 -
Rwork0.348 755 -
obs--98.39 %
Refinement TLS params.Method: refined / Origin x: -22.9738 Å / Origin y: -11.5856 Å / Origin z: 14.1704 Å
111213212223313233
T0.0557 Å2-0.0027 Å2-0.0169 Å2-0.0169 Å20.0042 Å2--0.0305 Å2
L0.2159 °2-0.2168 °20.2701 °2-0.7798 °2-0.2993 °2--1.1345 °2
S-0.0341 Å °0.0075 Å °0.057 Å °0.0235 Å °-0.0687 Å °-0.0002 Å °-0.0947 Å °-0.0011 Å °0.1028 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 197
2X-RAY DIFFRACTION1A303

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