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- PDB-6dcz: The N-terminal domain of PA endonuclease from the influenza H1N1 ... -

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Basic information

Entry
Database: PDB / ID: 6dcz
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-4-oxo-4H-pyran-2-carboxylic acid
ComponentsPolymerase acidic protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / Endonuclease / Influenza / PA domain / 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
3-hydroxy-4-oxo-4H-pyran-2-carboxylic acid / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsDick, B.L. / Morrison, C.N. / Cohen, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098435 United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease.
Authors: Credille, C.V. / Dick, B.L. / Morrison, C.N. / Stokes, R.W. / Adamek, R.N. / Wu, N.C. / Wilson, I.A. / Cohen, S.M.
History
DepositionMay 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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

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Assembly

Deposited unit
A: Polymerase acidic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7354
Polymers22,4691
Non-polymers2663
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-7 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.840, 75.840, 121.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Polymerase acidic protein / RNA-directed RNA polymerase subunit P2


Mass: 22468.666 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-198)
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)
References: UniProt: C3W5S0, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-G5Y / 3-hydroxy-4-oxo-4H-pyran-2-carboxylic acid


Mass: 156.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 308 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG4000, 100 mM Tris, pH 8.0, 200 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.89→30.33 Å / Num. obs: 4826 / % possible obs: 95.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 12.5
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 773 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4AWM

4awm


Resolution: 2.89→28.89 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.85 / SU B: 17.7 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.495 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27586 473 9.8 %RANDOM
Rwork0.19963 ---
obs0.20684 4332 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.918 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.23 Å2-0 Å2
2---0.47 Å2-0 Å2
3---1.51 Å2
Refinement stepCycle: 1 / Resolution: 2.89→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 13 4 1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0141537
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171370
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.6722062
X-RAY DIFFRACTIONr_angle_other_deg0.8441.6373215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8721.18393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.41815291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4211514
X-RAY DIFFRACTIONr_chiral_restr0.0590.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021705
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02300
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_it2.874.366718
X-RAY DIFFRACTIONr_mcbond_other2.8584.361717
X-RAY DIFFRACTIONr_mcangle_it4.6536.53894
X-RAY DIFFRACTIONr_mcangle_other4.6516.536895
X-RAY DIFFRACTIONr_scbond_it3.0034.632819
X-RAY DIFFRACTIONr_scbond_other3.0084.636816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7696.8121167
X-RAY DIFFRACTIONr_long_range_B_refined7.28749.1261793
X-RAY DIFFRACTIONr_long_range_B_other7.28849.1331792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.891→2.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 35 -
Rwork0.289 310 -
obs--99.42 %

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