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- PDB-2jh8: The structure of bluetongue virus VP4 reveals a multifunctional R... -

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Basic information

Entry
Database: PDB / ID: 2jh8
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


viral outer capsid / viral capsid
Similarity search - Function
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
GUANINE / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Core protein VP4 / Core protein VP4
Similarity search - Component
Biological speciesBLUETONGUE VIRUS 10
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.22 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Other / Source and taxonomy / Category: entity_src_gen / pdbx_database_status
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _pdbx_database_status.status_code_sf
Revision 2.0Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VP4 CORE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2624
Polymers75,5021
Non-polymers7603
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)75.055, 75.055, 419.834
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) / Strain: BTV-10 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P07132, UniProt: Q65751*PLUS
#2: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2
#3: Chemical ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5O
Compound detailsTHE VP4 PROTEIN IS ONE OF THE FIVE PROTEINS (WITH VP1, VP3, VP6 AND VP7) WHICH FORMS THE INNER ...THE VP4 PROTEIN IS ONE OF THE FIVE PROTEINS (WITH VP1, VP3, VP6 AND VP7) WHICH FORMS THE INNER CAPSID OF THE VIRUS. VP4 CAPS VIRAL RNA.

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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: 2.26 Å3/Da / Density % sol: 45.68 %
Description: THIS STRUCTURE IS A LIGAND (7MGDP) SOAK. THE ADOHCY (HIGH RESOLUTION) AND 7MGDP STRUCTURES WERE ISOMORPHOUS SO THIS STRUCTURE WAS SOLVED FROM THE ADOHCY - IT DID NOT REQUIR MOLECULAR ...Description: THIS STRUCTURE IS A LIGAND (7MGDP) SOAK. THE ADOHCY (HIGH RESOLUTION) AND 7MGDP STRUCTURES WERE ISOMORPHOUS SO THIS STRUCTURE WAS SOLVED FROM THE ADOHCY - IT DID NOT REQUIR MOLECULAR REPLACEMENT. VP4-7MGDP CRYSTALS ARE ISOMORPHOUS WITH VP4-ADOHCY CRYSTALS
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: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 30, 2005 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 11731 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 18.2 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 12.4
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 3.22→25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.34125 590 4.8 %RANDOM
Rwork0.24553 ---
obs0.24553 11731 100 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 72.907 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20.81 Å20 Å2
2--1.62 Å20 Å2
3----2.43 Å2
Refine analyzeLuzzati coordinate error obs: 0.736 Å / Luzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.776 Å
Refinement stepCycle: LAST / Resolution: 3.22→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 51 0 5091
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.956
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.5371.5
X-RAY DIFFRACTIONc_mcangle_it0.9422
X-RAY DIFFRACTIONc_scbond_it1.1893
X-RAY DIFFRACTIONc_scangle_it1.9694.5
LS refinement shellResolution: 3.217→3.299 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 42 39.9 %
Rwork0.294 821 -
obs--100 %

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