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- PDB-5fmz: Crystal structure of Influenza B polymerase with bound 5' vRNA -

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Basic information

Entry
Database: PDB / ID: 5fmz
TitleCrystal structure of Influenza B polymerase with bound 5' vRNA
Components
  • 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'
  • POLYMERASE ACIDIC PROTEIN
  • POLYMERASE BASIC PROTEIN 2
  • RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
KeywordsTRANSCRIPTION / INFLUENZA B VIRUS RNA-DEPENDENT RNA POLYMERASE / HETEROTRIMER / VIRAL RNA / VRNA 5' END.
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: 3.4 Å
AuthorsGuilligay, D. / Cusack, S.
Citation
Journal: Mol.Cell / Year: 2016
Title: Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of Pb2 Domains.
Authors: Thierry, E. / Guilligay, D. / Kosinski, J. / Bock, T. / Gaudon, S. / Round, A. / Pflug, A. / Hengrung, N. / El Omari, K. / Baudin, F. / Hart, D.J. / Beck, M. / Cusack, S.
#1: Journal: Nature / Year: 2014
Title: Structure of Influenza a Polymerase Bound to the Viral RNA Promoter.
Authors: Pflug, A. / Guilligay, D. / Reich, S. / Cusack, S.
History
DepositionNov 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: POLYMERASE ACIDIC PROTEIN
B: RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
C: POLYMERASE BASIC PROTEIN 2
D: POLYMERASE ACIDIC PROTEIN
E: RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
F: POLYMERASE BASIC PROTEIN 2
H: 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'
V: 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)533,5158
Polymers533,5158
Non-polymers00
Water00
1
D: POLYMERASE ACIDIC PROTEIN
E: RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
F: POLYMERASE BASIC PROTEIN 2
H: 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)266,7574
Polymers266,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38110 Å2
ΔGint-232.4 kcal/mol
Surface area87760 Å2
MethodPISA
2
A: POLYMERASE ACIDIC PROTEIN
B: RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT
C: POLYMERASE BASIC PROTEIN 2
V: 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)266,7574
Polymers266,7574
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37780 Å2
ΔGint-227 kcal/mol
Surface area87230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.570, 200.540, 133.130
Angle α, β, γ (deg.)90.00, 107.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein POLYMERASE ACIDIC PROTEIN / INFLUENZA B POLYMERASE PA SUBUNIT


Mass: 85822.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA B VIRUS (B/MEMPHIS/13/2003) / Plasmid: PKL-PBAC / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q5V8Z9
#2: Protein RNA-DIRECTED RNA POLYMERASE CATALYTIC SUBUNIT / INFLUENZA B POLYMERASE PB1 SUBUNIT


Mass: 86207.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA B VIRUS (B/MEMPHIS/13/2003) / Plasmid: PKL-PBAC / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q5V8Y6, RNA-directed RNA polymerase
#3: Protein POLYMERASE BASIC PROTEIN 2 / INFLUENZA B POLYMERASE PB2 SUBUNIT


Mass: 90844.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA B VIRUS (B/MEMPHIS/13/2003) / Plasmid: PKL-PBAC / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: Q5V8X3
#4: RNA chain 5'-R(*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP)-3' / VRNA 5' END


Mass: 3883.408 Da / Num. of mol.: 2 / Fragment: FIRST 12 NUCLEOTIDES / Source method: obtained synthetically / Source: (synth.) INFLUENZA B VIRUS (B/MEMPHIS/13/2003)
Sequence detailsN-TERMINAL EXTENSION, HIS-TAG AND LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE N-TERMINAL ...N-TERMINAL EXTENSION, HIS-TAG AND LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE N-TERMINAL EXTENSION, LINKER. C-TERMINAL EXTENSION, LINKER AND TEV SITE N-TERMINAL EXTENSION, LINKER. C-TERMINAL EXTENSION, LINKER, STREP-TAG AND TEV SITE

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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: 3.05 Å3/Da / Density % sol: 59.7 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M KCL, 10 MM MGCL2, 50 MM TRIS-HCL PH 8.5 AND 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07228
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07228 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 86591 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.37 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 7.83
Reflection shellResolution: 3.4→3.55 Å / Redundancy: 6.11 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.66 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4WSA

4wsa


Resolution: 3.4→126.83 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.878 / SU B: 46.772 / SU ML: 0.674 / Cross valid method: THROUGHOUT / ESU R Free: 0.611 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27696 2595 3 %RANDOM
Rwork0.2553 ---
obs0.25595 83996 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.884 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å2-0.12 Å2
2---9.99 Å20 Å2
3---7.19 Å2
Refinement stepCycle: LAST / Resolution: 3.4→126.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34112 524 0 0 34636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01935345
X-RAY DIFFRACTIONr_bond_other_d0.0010.0233992
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.95547719
X-RAY DIFFRACTIONr_angle_other_deg0.853378433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68654265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.48124.3581565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.104156570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.11615228
X-RAY DIFFRACTIONr_chiral_restr0.0530.25239
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02139123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027911
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6211.17617119
X-RAY DIFFRACTIONr_mcbond_other1.61911.17617118
X-RAY DIFFRACTIONr_mcangle_it2.9116.75721364
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.15811.17818226
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 165 -
Rwork0.383 6197 -
obs--99.5 %

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