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- PDB-2qj1: Crystal structure of infectious bursal disease virus VP1 polymera... -

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Basic information

Entry
Database: PDB / ID: 2qj1
TitleCrystal structure of infectious bursal disease virus VP1 polymerase incubated with an oligopeptide mimicking the VP3 C-terminus
ComponentsInfectious bursal disease virus VP1 polymerase
KeywordsTRANSFERASE / infectious bursal disease virus / ibdv / birnavirus / polymerase / vp1 / vp3 / activation
Function / homology
Function and homology information


virion component => GO:0044423 / 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 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
Protein VP1 / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesInfectious bursal disease virus (Gumboro virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.48 Å
AuthorsGarriga, D. / Navarro, A. / Querol-Audi, J. / Abaitua, F. / Rodriguez, J.F. / Verdaguer, N.
CitationJournal: To be Published
Title: Unprecedented activation mechanism of a non-canonical RNA-dependent RNA polymerase
Authors: Garriga, D. / Navarro, A. / Querol-Audi, J. / Abaitua, F. / Rodriguez, J.F. / Verdaguer, N.
History
DepositionJul 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 400COMPOUND THE VP3 PEPTIDE WAS CRYSTALLIZED WITH THE VP1 PROTEIN, BUT IT APPEARS POORLY ORDERED IN ...COMPOUND THE VP3 PEPTIDE WAS CRYSTALLIZED WITH THE VP1 PROTEIN, BUT IT APPEARS POORLY ORDERED IN THE STRUCTURE OF THE COMPLEX, AS ONLY A WEAK ELONGATED EXTRA DENSITY WAS DETECTED. THIS DENSITY COULD BE INTERPRETED AS DUE TO THE PRESENCE OF ABOUT FIVE AMINO ACIDS IN AN EXTENDED CONFORMATION, BUT THE AUTHORS WERE NOT ABLE TO ASSIGN ANY RESIDUE TO IT.
Remark 999SEQUENCE AUTHORS STATE THAT RESIDUE AT POSITION 4 IS INDEED VALINE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Infectious bursal disease virus VP1 polymerase


Theoretical massNumber of molelcules
Total (without water)94,6521
Polymers94,6521
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.913, 121.913, 359.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThis molecule is a monomer.

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Components

#1: Protein Infectious bursal disease virus VP1 polymerase / P2 / VP1


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: VP1 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High Five (TM) cells / References: UniProt: Q82629, UniProt: Q9Q6Q5*PLUS

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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: 4.07 Å3/Da / Density % sol: 69.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10-12% PEG 3350, 0.3-0.5M LiNO3, pH 6.5-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.48→40 Å / Num. all: 20344 / Num. obs: 20344 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.11 / Net I/σ(I): 10.3
Reflection shellResolution: 3.5→3.65 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.54 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ProDCdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VP1 polymease apo form structure (PDB code 2PUS)

2pus


Resolution: 3.48→19.98 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.852 / SU B: 59.429 / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1039 5.1 %RANDOM
Rwork0.241 ---
all0.245 20344 --
obs0.243 20247 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.518 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 3.48→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5927 0 0 0 5927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226046
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9788218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7895757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57524.309246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.33151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0941533
X-RAY DIFFRACTIONr_chiral_restr0.0680.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024545
X-RAY DIFFRACTIONr_nbd_refined0.1980.22815
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2163
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.234
X-RAY DIFFRACTIONr_mcbond_it0.4151.53898
X-RAY DIFFRACTIONr_mcangle_it0.68526122
X-RAY DIFFRACTIONr_scbond_it0.61932462
X-RAY DIFFRACTIONr_scangle_it1.0364.52096
LS refinement shellResolution: 3.484→3.572 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 85 -
Rwork0.242 1371 -
obs-1456 98.58 %

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