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- PDB-5eg8: The cap binding site of influenza virus protein PB2 as a drug target -

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Basic information

Entry
Database: PDB / ID: 5eg8
TitleThe cap binding site of influenza virus protein PB2 as a drug target
ComponentsPolymerase basic protein 2
KeywordsVIRAL PROTEIN / PB2 cap native
Function / homology
Function and homology information


cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / virion component / DNA-templated transcription / host cell nucleus / RNA binding
Similarity search - Function
PB2, C-terminal / : / : / Influenza RNA polymerase PB2 middle domain / Influenza RNA polymerase PB2 C-terminal domain / : / Influenza RNA polymerase PB2 6th domain / : / Influenza RNA polymerase PB2 CAP binding domain / : / Influenza RNA polymerase PB2 helical domain
Similarity search - Domain/homology
THIOCYANATE ION / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsLiu, Y. / Zheng, X. / Severin, C. / Rocha de Moura, T. / Li, K. / 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

Downloads & links

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Assembly

Deposited unit
A: Polymerase basic protein 2
B: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,42010
Polymers36,9552
Non-polymers4658
Water6,071337
1
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7105
Polymers18,4771
Non-polymers2324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7105
Polymers18,4771
Non-polymers2324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.611, 54.611, 196.486
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Polymerase basic protein 2


Mass: 18477.459 Da / Num. of mol.: 2 / Fragment: UNP residues 108-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/swine/Quebec/1257777/2010(H3N2))
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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG

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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: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→15 Å / Num. obs: 47547 / % possible obs: 97.2 % / Redundancy: 15.1 % / Rsym value: 0.071 / Net I/σ(I): 57.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CB4

4cb4


Resolution: 1.54→14.63 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.15 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1769 2546 5.1 %RANDOM
Rwork0.1217 ---
obs0.1244 47547 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 118.24 Å2 / Biso mean: 25.333 Å2 / Biso min: 7.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å2-0 Å2
2---0.2 Å2-0 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 1.54→14.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 24 338 2942
Biso mean--39.74 39.38 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192794
X-RAY DIFFRACTIONr_bond_other_d0.0010.022769
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.9563749
X-RAY DIFFRACTIONr_angle_other_deg1.30336352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.785358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.96922.879132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80515555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9931532
X-RAY DIFFRACTIONr_chiral_restr0.1380.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023181
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02679
X-RAY DIFFRACTIONr_mcbond_it3.4942.0361380
X-RAY DIFFRACTIONr_mcbond_other3.3952.0231370
X-RAY DIFFRACTIONr_mcangle_it4.1293.0541729
X-RAY DIFFRACTIONr_rigid_bond_restr5.44835563
X-RAY DIFFRACTIONr_sphericity_free48.449598
X-RAY DIFFRACTIONr_sphericity_bonded16.62455760
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 195 -
Rwork0.088 3384 -
all-3579 -
obs--96.39 %
Refinement TLS params.

S31: -0.0011 Å ° / S32: 0.0001 Å ° / T11: 0.0028 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S33 (Å °)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01960.00640.00150.00510.00310.01030.0007-0.0003-0.0005-0.001-0.00060.0002-0.00010.0001-0.00020.0031-0.00010.000115.82336.098611.0813
20.0147-0.0030.00250.0022-0.00290.00940.0010-0.0010.0009-0.0003-0-0.0006-0-0.00010.00320.00020.000238.75416.08521.6798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A321 - 483
2X-RAY DIFFRACTION2B321 - 483

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