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- PDB-4wrt: Crystal structure of Influenza B polymerase with bound vRNA promo... -

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Basic information

Entry
Database: PDB / ID: 4wrt
TitleCrystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2)
Components
  • (Influenza virus polymerase vRNA promoter ...) x 2
  • PA
  • PB2
  • RNA-directed RNA polymerase catalytic subunit
KeywordsTRANSFERASE/RNA / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression ...cap snatching / viral transcription / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / host cell mitochondrion / virion component / endonuclease activity / Hydrolases; Acting on ester bonds / host cell cytoplasm / symbiont-mediated suppression of host gene expression / viral translational frameshifting / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / Influenza RNA polymerase PB2 N-terminal region / Influenza RNA polymerase PB2 second domain / : / Influenza RNA polymerase PB2 middle domain ...Influenza RNA-dependent RNA polymerase subunit PB2 / PB2, C-terminal / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB1 / : / : / 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 / Polymerase acidic protein / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA / RNA (> 10) / Polymerase basic protein 2 / RNA-directed RNA polymerase catalytic subunit / Polymerase acidic protein
Similarity search - Component
Biological speciesInfluenza B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsReich, S. / Guilligay, D. / Pflug, A. / Cusack, S.
Citation
Journal: Nature / Year: 2014
Title: Structural insight into cap-snatching and RNA synthesis by influenza polymerase.
Authors: Reich, S. / Guilligay, D. / Pflug, A. / Malet, H. / Berger, I. / Crepin, T. / Hart, D. / Lunardi, T. / Nanao, M. / Ruigrok, R.W. / Cusack, S.
#1: Journal: To Be Published
Title: Crystal structure of influenza A polymerase bound to the viral RNA promoter
Authors: Pflug, A. / Guilligay, D. / Reich, S. / Cusack, S.
History
DepositionOct 25, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Jan 10, 2024Group: 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
R: Influenza virus polymerase vRNA promoter 3' end
V: Influenza virus polymerase vRNA promoter 5' end
A: PA
B: RNA-directed RNA polymerase catalytic subunit
C: PB2


Theoretical massNumber of molelcules
Total (without water)273,0165
Polymers273,0165
Non-polymers00
Water14,574809
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39100 Å2
ΔGint-250 kcal/mol
Surface area67500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.370, 207.370, 345.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-801-

HOH

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Components

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Influenza virus polymerase vRNA promoter ... , 2 types, 2 molecules RV

#1: RNA chain Influenza virus polymerase vRNA promoter 3' end


Mass: 5584.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza B virus
#2: RNA chain Influenza virus polymerase vRNA promoter 5' end


Mass: 4557.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Influenza B virus

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Protein , 3 types, 3 molecules ABC

#3: Protein PA


Mass: 85822.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal extension contains His-tag. C-terminal extension contains linker and residual TEV cleavage site
Source: (gene. exp.) Influenza B virus / Strain: B/Memphis/13/03 / Gene: PA / Plasmid: pKL-PBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Z9
#4: Protein RNA-directed RNA polymerase catalytic subunit


Mass: 86207.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal extension contains linker. C-terminal extension contains linker and residual TEV cleavage site
Source: (gene. exp.) Influenza B virus / Strain: B/Memphis/13/03 / Gene: PB1 / Plasmid: pKL-PBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase
#5: Protein PB2


Mass: 90844.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal extension contains linker. C-terminal extension contains linker, STRP tag and residual TEV cleavage site
Source: (gene. exp.) Influenza B virus / Strain: B/Memphis/13/03 / Gene: PB2 / Plasmid: pKL-PBac / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5V8X3

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Non-polymers , 1 types, 809 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.7 % / Description: Plate
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 1 M LiCl, 10% PEG 6000 and 0.1 M bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 120050 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.252 / Net I/σ(I): 10.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.49 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WSA

4wsa


Resolution: 2.7→49.657 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 5930 4.94 %
Rwork0.1734 --
obs0.1753 120037 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→49.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13548 615 0 809 14972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314503
X-RAY DIFFRACTIONf_angle_d0.68319692
X-RAY DIFFRACTIONf_dihedral_angle_d13.7285606
X-RAY DIFFRACTIONf_chiral_restr0.0272186
X-RAY DIFFRACTIONf_plane_restr0.0032422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73070.36911770.28933776X-RAY DIFFRACTION100
2.7307-2.76280.31481800.26793753X-RAY DIFFRACTION100
2.7628-2.79650.29192010.2463740X-RAY DIFFRACTION100
2.7965-2.83190.27861790.23563761X-RAY DIFFRACTION100
2.8319-2.86920.30062110.24163724X-RAY DIFFRACTION100
2.8692-2.90850.29042050.23463722X-RAY DIFFRACTION100
2.9085-2.950.29371930.22973780X-RAY DIFFRACTION100
2.95-2.9940.28392210.22563724X-RAY DIFFRACTION100
2.994-3.04080.28381940.21613748X-RAY DIFFRACTION100
3.0408-3.09070.24951930.21323759X-RAY DIFFRACTION100
3.0907-3.14390.26151840.20743793X-RAY DIFFRACTION100
3.1439-3.20110.27261950.20793743X-RAY DIFFRACTION100
3.2011-3.26270.25732060.20073761X-RAY DIFFRACTION100
3.2627-3.32920.2592040.19673779X-RAY DIFFRACTION100
3.3292-3.40160.24132030.19413748X-RAY DIFFRACTION100
3.4016-3.48070.22281930.18773781X-RAY DIFFRACTION100
3.4807-3.56770.23431730.1763809X-RAY DIFFRACTION100
3.5677-3.66420.22081990.17063799X-RAY DIFFRACTION100
3.6642-3.7720.22772190.1593765X-RAY DIFFRACTION100
3.772-3.89370.17742090.15343758X-RAY DIFFRACTION100
3.8937-4.03280.16741880.13763833X-RAY DIFFRACTION100
4.0328-4.19420.16361810.13193814X-RAY DIFFRACTION100
4.1942-4.38490.15942260.12993793X-RAY DIFFRACTION100
4.3849-4.6160.15411860.1273843X-RAY DIFFRACTION100
4.616-4.90490.14862050.12393817X-RAY DIFFRACTION100
4.9049-5.28330.17141970.13873852X-RAY DIFFRACTION100
5.2833-5.81420.1831950.14953880X-RAY DIFFRACTION100
5.8142-6.65380.18521870.15813928X-RAY DIFFRACTION100
6.6538-8.37660.16982110.15653946X-RAY DIFFRACTION100
8.3766-49.66540.17322150.18444178X-RAY DIFFRACTION100

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