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- PDB-5eg9: The cap binding site of influenza virus protein PB2 as a drug target -

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Basic information

Entry
Database: PDB / ID: 5eg9
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


virion component => GO:0044423 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / 7-methylguanosine mRNA capping / viral RNA genome replication / RNA-dependent RNA polymerase activity / 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
Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,9952
Polymers40,9952
Non-polymers00
Water1,13563
1
A: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)20,4981
Polymers20,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Polymerase basic protein 2


Theoretical massNumber of molelcules
Total (without water)20,4981
Polymers20,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.133, 109.010, 39.655
Angle α, β, γ (deg.)90.000, 90.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Polymerase basic protein 2 / RNA-directed RNA polymerase subunit P3


Mass: 20497.707 Da / Num. of mol.: 2 / Fragment: UNP residues 322-420, 428-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Chicken/Hong Kong/YU22/2002 H5N1 genotype Z / Gene: PB2 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6DNL8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
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: Jul 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 11663 / % possible obs: 87.7 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.066 / Rrim(I) all: 0.097 / Χ2: 4.658 / Net I/av σ(I): 21.055 / Net I/σ(I): 13.1 / Num. measured all: 21876
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.341.70.1946410.9090.1830.2672.52392.6
2.34-2.381.80.196490.8660.1810.2632.11495.7
2.38-2.431.70.1596590.8510.1540.2222.23594.5
2.43-2.481.80.1376880.9310.1290.1892.64693.6
2.48-2.531.80.1576350.8520.1510.2187.17796.7
2.53-2.591.80.1356840.9190.1260.1853.2195.1
2.59-2.661.80.1296600.9220.1220.1783.41494.2
2.66-2.731.80.1176640.9340.1110.1623.7795.7
2.73-2.811.70.1086740.940.1030.1493.51995.9
2.81-2.91.80.0936460.9560.0880.1283.49493.6
2.9-31.80.0976580.9540.0910.1335.12995.4
3-3.121.80.0856860.9660.0790.1164.57394.5
3.12-3.261.80.096520.940.0840.1235.72995
3.26-3.441.80.0826510.9590.0750.1125.64393.5
3.44-3.651.70.0663210.9790.0630.0915.73544.8
3.65-3.931.60.0763130.970.0720.1059.75744.8
3.93-4.331.80.0535140.9880.0480.0724.77374.7
4.33-4.951.80.056600.9860.0450.0687.39991.4
4.95-6.241.90.0486340.9850.0430.0645.39190.1
6.24-501.90.0485990.9860.0440.0668.51182.5

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Processing

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

5eg8


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.899 / SU B: 16.035 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.59 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 602 4.9 %RANDOM
Rwork0.1911 ---
obs0.1945 11661 87.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.37 Å2 / Biso mean: 34.452 Å2 / Biso min: 14.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å2-0 Å20.34 Å2
2--2.42 Å20 Å2
3---0.2 Å2
Refinement stepCycle: final / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2453 0 0 63 2516
Biso mean---30.18 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192494
X-RAY DIFFRACTIONr_bond_other_d0.0010.022479
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9593342
X-RAY DIFFRACTIONr_angle_other_deg0.82135686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56923.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59715483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9991524
X-RAY DIFFRACTIONr_chiral_restr0.1030.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02585
X-RAY DIFFRACTIONr_mcbond_it2.4763.0111255
X-RAY DIFFRACTIONr_mcbond_other2.4583.011254
X-RAY DIFFRACTIONr_mcangle_it4.0154.5051567
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 39 -
Rwork0.22 871 -
all-910 -
obs--87.16 %
Refinement TLS params.

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 °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6520.03430.08020.141-0.14870.3191-0.00940.00130.0107-0.03370.0109-0.01810.0483-0.0161-0.00150.0202-0.00350.00070.00510.0010.00744.25470.013215.0227
20.5060.1324-0.12090.20610.04350.2894-0.01720.0191-0.0294-0.0244-0.00430.0049-0.03240.00480.02150.0137-0.0017-0.00420.00680.0020.00614.176527.98429.9915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A322 - 478
2X-RAY DIFFRACTION2B322 - 477

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