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- PDB-7xme: Structure of Influenza A virus polymerase basic protein 2 (PB2) w... -

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Basic information

Entry
Database: PDB / ID: 7xme
TitleStructure of Influenza A virus polymerase basic protein 2 (PB2) with an azazindole derivative
ComponentsPolymerase basic protein 2
KeywordsRNA BINDING PROTEIN / Inhibitor / Complex
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 / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / symbiont-mediated suppression of host gene expression / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription ...cap snatching / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / symbiont-mediated suppression of host gene expression / viral RNA genome replication / RNA-directed 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 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain / : / Influenza RNA polymerase PB2 C-terminal domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / 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
Chem-GIH / IODIDE ION / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.521 Å
AuthorsZhang, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Discovery of a novel azaindole derivatives targeting the influenza PB2 cap binding region
Authors: Zhang, Z. / Liu, X.
History
DepositionApr 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,96912
Polymers75,5044
Non-polymers2,4658
Water97354
1
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4923
Polymers18,8761
Non-polymers6162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4923
Polymers18,8761
Non-polymers6162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4923
Polymers18,8761
Non-polymers6162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4923
Polymers18,8761
Non-polymers6162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.791, 31.306, 114.552
Angle α, β, γ (deg.)90.000, 95.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-311-

HOH

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Components

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


Mass: 18875.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Victoria/3/1975(H3N2))
Strain: A/Victoria/3/1975 H3N2 / Gene: PB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31345
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-GIH / (2~{S},3~{S})-3-[[5-dimethoxyphosphoryl-4-(5-fluoranyl-1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-yl]amino]bicyclo[2.2.2]octane-2-carboxylic acid


Mass: 489.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H25FN5O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: Soudium,BIS-Tris propane pH 8.5,PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jan 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.521→88.016 Å / Num. obs: 21874 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.993 / Net I/σ(I): 8.6
Reflection shellResolution: 2.521→2.565 Å / Num. unique obs: 1099 / CC1/2: 0.774

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P1U

4p1u


Resolution: 2.521→45.958 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3297 1063 4.87 %
Rwork0.2501 20780 -
obs0.2539 21843 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 196.35 Å2 / Biso mean: 39.0721 Å2 / Biso min: 23.99 Å2
Refinement stepCycle: final / Resolution: 2.521→45.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 236 54 5107
Biso mean--30.3 33.49 -
Num. residues----618
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5213-2.6360.39821230.3052591
2.636-2.7750.41221290.31322539
2.775-2.94880.38041320.29362551
2.9488-3.17640.35271350.27532578
3.1764-3.4960.34711230.25912586
3.496-4.00160.32731260.22452588
4.0016-5.04060.27561580.20172608
5.0406-90.29941370.24762739
Refinement TLS params.Method: refined / Origin x: -24.1241 Å / Origin y: -9.2295 Å / Origin z: 28.1097 Å
111213212223313233
T0.4886 Å2-0.0154 Å20.1653 Å2-0.1766 Å2-0.019 Å2--0.2861 Å2
L0.2612 °2-0.0561 °20.0041 °2-0.1832 °2-0.0922 °2--0.1093 °2
S-0.0155 Å °0.0132 Å °-0.0568 Å °-0.0169 Å °0.0061 Å °0.0291 Å °0.0467 Å °-0.056 Å °0.0252 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA21 - 182
2X-RAY DIFFRACTION1allB21 - 182
3X-RAY DIFFRACTION1allC21 - 183
4X-RAY DIFFRACTION1allD21 - 183
5X-RAY DIFFRACTION1allF1 - 6
6X-RAY DIFFRACTION1allS2 - 71
7X-RAY DIFFRACTION1allE3 - 6

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