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

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Basic information

Entry
Database: PDB / ID: 6dcy
TitleThe N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 5-hydroxy-2-methyl-4-oxo-4H-pyran-3-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 / 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-G5V / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 / 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)22,7494
Polymers22,4691
Non-polymers2803
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-7 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.540, 75.540, 120.360
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-G5V / 5-hydroxy-2-methyl-4-oxo-4H-pyran-3-carboxylic acid


Mass: 170.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.21 Å3/Da / Density % sol: 44.24 % / Description: Octahedron
Crystal growTemperature: 306 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5 mM inhibitor, 25-40% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→37.77 Å / Num. obs: 12849 / % possible obs: 100 % / Redundancy: 16.9 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.1
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 974 / % possible all: 100

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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: 2.08→37.77 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.26 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.203 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2714 611 4.8 %RANDOM
Rwork0.22468 ---
obs0.22714 12045 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.595 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.22 Å2-0 Å2
2---0.43 Å2-0 Å2
3---1.41 Å2
Refinement stepCycle: 1 / Resolution: 2.08→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 14 11 1493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141509
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171337
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.6752023
X-RAY DIFFRACTIONr_angle_other_deg0.9611.6393137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1445173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45821.18393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92815285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9311514
X-RAY DIFFRACTIONr_chiral_restr0.070.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021669
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
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_it3.4914.249701
X-RAY DIFFRACTIONr_mcbond_other3.4854.244700
X-RAY DIFFRACTIONr_mcangle_it4.9366.335871
X-RAY DIFFRACTIONr_mcangle_other4.9346.341872
X-RAY DIFFRACTIONr_scbond_it4.7264.806808
X-RAY DIFFRACTIONr_scbond_other4.7244.807809
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7996.9821153
X-RAY DIFFRACTIONr_long_range_B_refined8.5648.6921735
X-RAY DIFFRACTIONr_long_range_B_other8.55748.7031736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 50 -
Rwork0.257 859 -
obs--99.89 %

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