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- PDB-9i2o: PB2 cap-binding domain of human pathogenic influenza A virus H5N1... -

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Basic information

Entry
Database: PDB / ID: 9i2o
TitlePB2 cap-binding domain of human pathogenic influenza A virus H5N1 in complex with m7GTP
ComponentsPolymerase basic protein 2
KeywordsRNA BINDING PROTEIN / avian influenza / RNA capping / polymerase complex / drug development
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 / 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
7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE / Polymerase basic protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsFalke, S. / Lewe, P. / Witt, S. / Wrenger, C. / Meents, A.
Funding support Germany, 2items
OrganizationGrant numberCountry
Helmholtz Association Germany
German Federal Ministry for Education and Research Germany
CitationJournal: To Be Published
Title: PB2 cap-binding domain of human pathogenic influenza A virus H5N1 in complex with m7GTP
Authors: Falke, S. / Lewe, P. / Witt, S. / Wrenger, C. / Meents, A.
History
DepositionJan 21, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase basic protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9142
Polymers21,3751
Non-polymers5391
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-3 kcal/mol
Surface area8890 Å2
Unit cell
Length a, b, c (Å)81.750, 81.750, 55.009
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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


Mass: 21374.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: PB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6DNL8
#2: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: The PB2 cap-binding domain (8 mg/ml) in complex with m7GTP was mixed with crystallization solution (20% w/v PEG 6000, 1 M lithium chloride, 0.1 M tri-sodium citrate at pH 4.0) at a ratio of ...Details: The PB2 cap-binding domain (8 mg/ml) in complex with m7GTP was mixed with crystallization solution (20% w/v PEG 6000, 1 M lithium chloride, 0.1 M tri-sodium citrate at pH 4.0) at a ratio of 3:2 and incubated in a sitting drop vapor diffusion plate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03327 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03327 Å / Relative weight: 1
ReflectionResolution: 1.72→43.44 Å / Num. obs: 43754 / % possible obs: 100 % / Redundancy: 10.4 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.014 / Net I/σ(I): 9.54
Reflection shellResolution: 1.72→1.82 Å / Num. unique obs: 3589 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
PHENIX1.21.2-5419_9999refinement
XDSdata reduction
PHENIX1.21.2-5419_9999phasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→43.44 Å / SU ML: 0.2888 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4893
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 3934 9 %
Rwork0.1824 39774 -
obs0.1846 43708 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.79 Å2
Refinement stepCycle: LAST / Resolution: 1.72→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 33 71 1394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761386
X-RAY DIFFRACTIONf_angle_d0.7941872
X-RAY DIFFRACTIONf_chiral_restr0.0598207
X-RAY DIFFRACTIONf_plane_restr0.0079244
X-RAY DIFFRACTIONf_dihedral_angle_d16.4443547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.40291390.4171349X-RAY DIFFRACTION96.81
1.74-1.760.43121360.3761446X-RAY DIFFRACTION99.5
1.76-1.780.36441420.33871423X-RAY DIFFRACTION99.55
1.78-1.810.33361420.32191412X-RAY DIFFRACTION100
1.81-1.840.3241400.30661424X-RAY DIFFRACTION99.94
1.84-1.860.31161400.27871447X-RAY DIFFRACTION100
1.86-1.890.30191400.27971413X-RAY DIFFRACTION100
1.89-1.920.27261380.28781387X-RAY DIFFRACTION100
1.92-1.960.25621460.24931433X-RAY DIFFRACTION99.87
1.96-1.990.27361400.23581443X-RAY DIFFRACTION100
1.99-2.030.26131410.19251420X-RAY DIFFRACTION100
2.03-2.070.2191420.19711401X-RAY DIFFRACTION100
2.07-2.120.19631430.1861421X-RAY DIFFRACTION99.94
2.12-2.170.2811370.16941421X-RAY DIFFRACTION100
2.17-2.220.27641420.18291441X-RAY DIFFRACTION99.87
2.22-2.280.21711420.17791417X-RAY DIFFRACTION100
2.28-2.350.20171300.16781439X-RAY DIFFRACTION100
2.35-2.420.23721410.18251415X-RAY DIFFRACTION100
2.42-2.510.16351330.18311408X-RAY DIFFRACTION100
2.51-2.610.21621460.17851444X-RAY DIFFRACTION100
2.61-2.730.20581500.17871433X-RAY DIFFRACTION100
2.73-2.870.23391360.1971393X-RAY DIFFRACTION100
2.87-3.050.22391440.18231438X-RAY DIFFRACTION99.87
3.05-3.280.18291320.17841419X-RAY DIFFRACTION100
3.29-3.620.18581270.171440X-RAY DIFFRACTION100
3.62-4.140.16021500.14931410X-RAY DIFFRACTION100
4.14-5.210.15621490.14281414X-RAY DIFFRACTION99.94
5.22-43.440.18361460.16621423X-RAY DIFFRACTION100

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