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- PDB-2jh9: The structure of bluetongue virus VP4 reveals a multifunctional R... -

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Basic information

Entry
Database: PDB / ID: 2jh9
TitleThe structure of bluetongue virus VP4 reveals a multifunctional RNA- capping production-line
ComponentsVP4 CORE PROTEIN
KeywordsVIRAL PROTEIN / GUANYLYLTRANSFERASE / VIRAL CAPPING ENZYME / CORE PROTEIN / VIRION PROTEIN / METHYLTRANSFERASE
Function / homology
Function and homology information


Orbivirus VP4 core protein, C-terminal domain / Orbivirus VP4 core / Orbivirus VP4 core, C-terminal / Orbivirus VP4 core protein / Monooxygenase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Orbivirus VP4 core protein, C-terminal domain / Orbivirus VP4 core / Orbivirus VP4 core, C-terminal / Orbivirus VP4 core protein / Monooxygenase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GUANINE / Core protein VP4
Similarity search - Component
Biological speciesBLUETONGUE VIRUS 10
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å
AuthorsSutton, G. / Grimes, J.M. / Stuart, D.I. / Roy, P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Bluetongue Virus Vp4 is an RNA-Capping Assembly Line.
Authors: Sutton, G. / Grimes, J.M. / Stuart, D.I. / Roy, P.
History
DepositionFeb 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 23, 2015Group: Source and taxonomy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP4 CORE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3274
Polymers75,5021
Non-polymers8253
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.539, 75.539, 423.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein VP4 CORE PROTEIN / BLUETONGUE VIRUS VP4


Mass: 75501.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BLUETONGUE VIRUS 10 (ISOLATE USA) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P07132
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O

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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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growpH: 7.7
Details: 100 MM IMIDAZOLE PH 8.0, 2%-8% PROPAN-2-OL, 0-250 MM NACL, 50 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 2, 2004 / Details: MIRROR
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 14194 / % possible obs: 96.9 % / Observed criterion σ(I): 2.5 / Redundancy: 11 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 19.5
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.5 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 3→25 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.842 / SU B: 71.804 / SU ML: 0.589 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.61 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.33 716 4.8 %RANDOM
Rwork0.248 ---
obs0.252 14194 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.44 Å2
Baniso -1Baniso -2Baniso -3
1-3.94 Å21.97 Å20 Å2
2--3.94 Å20 Å2
3----5.91 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 54 0 5094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225225
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.9677071
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3535609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59222.451257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.94815912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4961553
X-RAY DIFFRACTIONr_chiral_restr0.1240.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023978
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2660.22516
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23430
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4251.53142
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74324943
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.97132430
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6174.52128
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→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.428 42
Rwork0.289 920
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.5176-0.37810.53585.9786-0.83376.97560.54360.53810.88160.9057-0.5184-0.829-1.0150.9409-0.02520.49450.1424-0.07550.18890.23510.148107.74235.879181.502
29.43252.4667-2.78140.645-0.72730.82010.4904-0.6630.03640.3484-0.218-0.09260.2797-0.0023-0.27230.29410.22650.0370.1129-0.01610.036380.16628.487185.598
39.2445-3.9597-0.3477.1156-2.38829.99010.64380.13420.70571.184-0.4947-0.5505-1.66560.3686-0.14910.3329-0.1390.0599-0.0769-0.00180.040565.77135.611203.13
45.2397-0.9295-0.957.1869-2.33186.83730.1182-0.06970.11230.80310.11290.5161-0.1053-0.247-0.2311-0.0939-0.11030.1023-0.09280.00640.03358.5623.105202.789
56.7841-2.9298-3.77316.85752.10843.46860.75090.0404-0.73970.1183-0.54990.12750.636-0.1124-0.20110.07980.091-0.01790.00480.0422-0.07680.00718.474175.458
63.6836-1.54970.28053.0685-0.04811.27310.69321.62860.8358-0.3513-0.5226-0.3195-0.65220.0513-0.17070.14630.33520.14350.58140.40230.176593.76230.821163.642
77.8255-0.9123-1.13098.3801-2.498212.36050.74211.9388-0.8348-1.2115-0.71410.07291.4297-0.2104-0.0280.50920.3852-0.01410.96-0.00830.373692.21417.187151.859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 100
2X-RAY DIFFRACTION2A101 - 160
3X-RAY DIFFRACTION3A161 - 237
4X-RAY DIFFRACTION4A238 - 391
5X-RAY DIFFRACTION5A392 - 452
6X-RAY DIFFRACTION6A453 - 598
7X-RAY DIFFRACTION7A599 - 644

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