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- PDB-2pus: Unprecedented activation mechanism of a non-canonical RNA-depende... -

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Basic information

Entry
Database: PDB / ID: 2pus
TitleUnprecedented activation mechanism of a non-canonical RNA-dependent RNA polymerase
ComponentsIBDV VP1 RNA-dependant RNA polymerase
KeywordsTRANSFERASE / RNA POLYMERASE MOTIFS
Function / homology
Function and homology information


viral genome replication / virion component / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTP binding
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #80 / RNA-directed RNA polymerase, C-terminal domain superfamily, Avibirnavirus / Infectious bursal virus vp1 polymerase fold / Infectious bursal virus vp1 polymerase domain / Helix Hairpins - #300 / Birnavirus RNA-directed RNA polymerase, palm domain / RNA-directed RNA polymerase, C-terminal, birnavirus / RNA-directed RNA polymerase, thumb domain, birnavirus / RNA-directed RNA polymerase, palm domain superfamily, Birnavirus / RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus ...Rna Polymerase Sigma Factor; Chain: A - #80 / RNA-directed RNA polymerase, C-terminal domain superfamily, Avibirnavirus / Infectious bursal virus vp1 polymerase fold / Infectious bursal virus vp1 polymerase domain / Helix Hairpins - #300 / Birnavirus RNA-directed RNA polymerase, palm domain / RNA-directed RNA polymerase, C-terminal, birnavirus / RNA-directed RNA polymerase, thumb domain, birnavirus / RNA-directed RNA polymerase, palm domain superfamily, Birnavirus / RNA-directed RNA polymerase, thumb domain superfamily, Birnavirus / Birnavirus RNA dependent RNA polymerase (VP1), palm domain / Birnavirus RNA dependent RNA polymerase (VP1), thumb domain / Birnavirus RNA dependent RNA polymerase (VP1), C-terminal / RdRp of Birnaviridae dsRNA viruses catalytic domain profile. / Helix hairpin bin / Rna Polymerase Sigma Factor; Chain: A / Helix Hairpins / Helix non-globular / Special / Helix Hairpins / DNA/RNA polymerase superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase
Similarity search - Component
Biological speciesInfectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, Molec Replacement / Resolution: 2.4 Å
AuthorsGarriga, D. / Navarro, A. / Querol-Audi, J. / Abaitua, F. / Rodriguez, J.F. / Verdaguer, N.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Activation mechanism of a noncanonical RNA-dependent RNA polymerase.
Authors: Garriga, D. / Navarro, A. / Querol-Audi, J. / Abaitua, F. / Rodriguez, J.F. / Verdaguer, N.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999sequence The sequence is not available in UniProt database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IBDV VP1 RNA-dependant RNA polymerase


Theoretical massNumber of molelcules
Total (without water)94,6521
Polymers94,6521
Non-polymers00
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.171, 123.171, 362.216
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein IBDV VP1 RNA-dependant RNA polymerase


Mass: 94651.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bursal disease virus (Gumboro virus)
Genus: Avibirnavirus / Strain: Soroa / Gene: locus Q82629_IBDV / Plasmid: pFBHTc_VP1 846-879 / Production host: unidentified baculovirus / Strain (production host): HighFive cells (Invitrogen) / References: UniProt: Q9Q6Q5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 3

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Sample preparation

CrystalDensity Matthews: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10-12% PEG 3350, 0.3-0.5M LiNO3, pH 6.5 to 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
32001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-111.072
SYNCHROTRONESRF BM1621.8449, 1.6059
SYNCHROTRONESRF BM1631.776
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDMay 1, 2005
MAR CCD 165 mm2CCDNov 4, 2005
MAR CCD 165 mm3CCDNov 4, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
3Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0721
21.84491
31.60591
41.7761
ReflectionResolution: 2.4→40 Å / Num. all: 67915 / Num. obs: 67444 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Rsym value: 0.09 / Net I/σ(I): 21.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.27 / % possible all: 81.5

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARP+ AMoRephasing
RefinementMethod to determine structure: MAD, Molec Replacement / Resolution: 2.4→19.89 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.005 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26258 3094 5 %RANDOM
Rwork0.23401 ---
obs0.23544 58279 95.41 %-
all-61373 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5917 0 0 268 6185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226055
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9221.9788233
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2325761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82624.309246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.204151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3261533
X-RAY DIFFRACTIONr_chiral_restr0.0580.2919
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024561
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1610.22797
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2910.24164
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2327
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2511.53933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.45526137
X-RAY DIFFRACTIONr_scbond_it0.48932460
X-RAY DIFFRACTIONr_scangle_it0.8424.52096
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 156 -
Rwork0.27 2931 -
obs--66.83 %
Refinement TLS params.Method: refined / Origin x: -28.45 Å / Origin y: -38.31 Å / Origin z: 113.979 Å
111213212223313233
T-0.0613 Å20.0707 Å20.1413 Å2--0.2091 Å20.0959 Å2---0.0825 Å2
L1.198 °2-0.6013 °2-0.7241 °2-0.9524 °20.3213 °2--1.0617 °2
S0.0828 Å °-0.0108 Å °0.0945 Å °-0.201 Å °-0.0302 Å °-0.1662 Å °-0.1305 Å °0.078 Å °-0.0526 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 80434 - 811
2X-RAY DIFFRACTION1AB846 - 11131 - 268

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