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- PDB-4e5i: Crystal structure of avian influenza virus PAn bound to compound 4 -

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Basic information

Entry
Database: PDB / ID: 4e5i
TitleCrystal structure of avian influenza virus PAn bound to compound 4
ComponentsPolymerase protein PA
KeywordsVIRAL PROTEIN / TRANSCRIPTION / endonuclease domain / H5N1 subtype
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-0N9 / : / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.944 Å
AuthorsDuBois, R.M. / Slavish, P.J. / Webb, T.R. / White, S.W.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease.
Authors: Dubois, R.M. / Slavish, P.J. / Baughman, B.M. / Yun, M.K. / Bao, J. / Webby, R.J. / Webb, T.R. / White, S.W.
History
DepositionMar 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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 / struct_ref_seq_dif / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase protein PA
B: Polymerase protein PA
C: Polymerase protein PA
D: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,81724
Polymers87,6644
Non-polymers2,15320
Water00
1
A: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4546
Polymers21,9161
Non-polymers5385
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4546
Polymers21,9161
Non-polymers5385
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4546
Polymers21,9161
Non-polymers5385
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polymerase protein PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4546
Polymers21,9161
Non-polymers5385
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.332, 134.828, 126.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Polymerase protein PA / polymerase acidic protein


Mass: 21915.959 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Viet Nam/1203/2004 / Gene: PA / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5EP34
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-0N9 / 5-hydroxy-2-(1-methyl-1H-imidazol-4-yl)-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid


Mass: 236.184 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8N4O4
Sequence detailsPROTEIN COMPRISES UNP RESIDUES 1-50 AND 73-196 SEPARATED BY A GLY-GLY-SER LINKER.

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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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5 M ammonium sulfate, 2% PEG1500, 1 mM manganese chloride, 0.1 M Tris-Cl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.944→46.135 Å / Num. all: 23232 / Num. obs: 22442 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Biso Wilson estimate: 76.3 Å2 / Rmerge(I) obs: 0.071 / Χ2: 1.11 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.944-3.065.30.48816900.935174.4
3.06-3.186.70.41421420.963192.4
3.18-3.328.20.33422480.954199.1
3.32-3.58.80.23322961.0721100
3.5-3.729.10.15223161.1931100
3.72-49.10.10722971.3511100
4-4.419.20.07723301.2131100
4.41-5.049.10.05723211.1651100
5.04-6.3590.05523501.1331100
6.35-46.1358.60.0324520.933199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E5E

4e5e


Resolution: 2.944→46.135 Å / Cor.coef. Fo:Fc: 0.883 / Cor.coef. Fo:Fc free: 0.861 / WRfactor Rfree: 0.3575 / WRfactor Rwork: 0.3093 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6224 / SU B: 31.342 / SU ML: 0.571 / SU Rfree: 0.5965 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3683 1143 5.1 %RANDOM
Rwork0.3199 ---
obs0.3224 22423 96.48 %-
all-23241 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 247.8 Å2 / Biso mean: 81.2933 Å2 / Biso min: 51.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å2-0 Å2
2---1.91 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.944→46.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5959 0 116 0 6075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226179
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.9618305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1775717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8623.333318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.609151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1271556
X-RAY DIFFRACTIONr_chiral_restr0.0610.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024676
X-RAY DIFFRACTIONr_mcbond_it0.4231.53601
X-RAY DIFFRACTIONr_mcangle_it0.7725815
X-RAY DIFFRACTIONr_scbond_it0.48732578
X-RAY DIFFRACTIONr_scangle_it0.8774.52490
LS refinement shellResolution: 2.944→3.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 83 -
Rwork0.4 1086 -
all-1169 -
obs--69.46 %

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