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- PDB-5eg7: The cap binding site of influenza virus protein PB2 as a drug target -

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Basic information

Entry
Database: PDB / ID: 5eg7
TitleThe cap binding site of influenza virus protein PB2 as a drug target
ComponentsPolymerase basic protein 2
KeywordsVIRAL PROTEIN / PB2 cap
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / viral RNA genome replication / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA polymerase PB2 CAP binding domain
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSeverin, C. / Rocha de Moura, T. / Liu, Y. / Li, K. / Zheng, X. / Luo, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: The cap-binding site of influenza virus protein PB2 as a drug target.
Authors: Severin, C. / Rocha de Moura, T. / Liu, Y. / Li, K. / Zheng, X. / Luo, M.
History
DepositionOct 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6693
Polymers18,0381
Non-polymers6312
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.262, 45.262, 156.451
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Polymerase basic protein 2


Mass: 18037.945 Da / Num. of mol.: 1 / Fragment: UNP residues 106-207, 215-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/swine/Quebec/1257777/2010(H3N2) / Gene: PB2 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G3LZH2
#2: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→31.356 Å / Num. obs: 31468 / % possible obs: 99.8 % / Redundancy: 10.4 % / Rsym value: 0.071 / Net I/σ(I): 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data collection
SCALAdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EG8

5eg8


Resolution: 1.4→31.356 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.918 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1834 1652 5 %RANDOM
Rwork0.1616 ---
obs0.1627 31451 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.12 Å2 / Biso mean: 14.531 Å2 / Biso min: 5.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20 Å2
2---0.04 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.4→31.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 39 162 1457
Biso mean--25.54 25.85 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191500
X-RAY DIFFRACTIONr_bond_other_d0.0010.021475
X-RAY DIFFRACTIONr_angle_refined_deg2.6311.9912039
X-RAY DIFFRACTIONr_angle_other_deg1.00233405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1745198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.03322.37359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47215293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0111515
X-RAY DIFFRACTIONr_chiral_restr0.150.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021724
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02355
X-RAY DIFFRACTIONr_mcbond_it1.6261.074744
X-RAY DIFFRACTIONr_mcbond_other1.6031.071743
X-RAY DIFFRACTIONr_mcangle_it2.5271.606958
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 112 -
Rwork0.275 2211 -
all-2323 -
obs--98.02 %
Refinement TLS params.Method: refined / Origin x: -21.1358 Å / Origin y: 5.8704 Å / Origin z: 11.4587 Å
111213212223313233
T0.0014 Å20.0013 Å2-0.0008 Å2-0.0051 Å20.0022 Å2--0.0029 Å2
L0.1531 °20.041 °20.0672 °2-0.0586 °2-0.0231 °2--0.0704 °2
S0.0089 Å °0.0131 Å °-0.0053 Å °-0.0027 Å °0.0006 Å °0.0014 Å °0.009 Å °0.003 Å °-0.0095 Å °

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