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- PDB-5g51: High resolution structure of the part of VP3 protein of Deformed ... -

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Basic information

Entry
Database: PDB / ID: 5g51
TitleHigh resolution structure of the part of VP3 protein of Deformed Wing Virus forming P-domain
ComponentsDWV-VP3-P-DOMAIN
KeywordsVIRAL PROTEIN / PICORNAVIRALES / PICORNAVIRALES IFLAVIRIDAE IFLAVIRUS DWV CAPSID P-DOMAIN JELLYROLL INHIBITOR ANTIVIRAL CATALYTIC SITE PROTEASE LIPASE ESTERASE RECEPTOR
Function / homology
Function and homology information


viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / structural molecule activity ...viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase ...Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesDEFORMED WING VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSkubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structure of deformed wing virus, a major honey bee pathogen.
Authors: Karel Škubník / Jiří Nováček / Tibor Füzik / Antonín Přidal / Robert J Paxton / Pavel Plevka /
Abstract: The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) ...The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) from the family , together with its vector, the mite , is likely the major threat to the world's honey bees. However, lack of knowledge of the atomic structures of iflaviruses has hindered the development of effective treatments against them. Here, we present the virion structures of DWV determined to a resolution of 3.1 Å using cryo-electron microscopy and 3.8 Å by X-ray crystallography. The C-terminal extension of capsid protein VP3 folds into a globular protruding (P) domain, exposed on the virion surface. The P domain contains an Asp-His-Ser catalytic triad that is, together with five residues that are spatially close, conserved among iflaviruses. These residues may participate in receptor binding or provide the protease, lipase, or esterase activity required for entry of the virus into a host cell. Furthermore, nucleotides of the DWV RNA genome interact with VP3 subunits. The capsid protein residues involved in the RNA binding are conserved among honey bee iflaviruses, suggesting a putative role of the genome in stabilizing the virion or facilitating capsid assembly. Identifying the RNA-binding and putative catalytic sites within the DWV virion structure enables future analyses of how DWV and other iflaviruses infect insect cells and also opens up possibilities for the development of antiviral treatments.
History
DepositionMay 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

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Assembly

Deposited unit
A: DWV-VP3-P-DOMAIN


Theoretical massNumber of molelcules
Total (without water)17,5361
Polymers17,5361
Non-polymers00
Water4,360242
1
A: DWV-VP3-P-DOMAIN

A: DWV-VP3-P-DOMAIN

A: DWV-VP3-P-DOMAIN

A: DWV-VP3-P-DOMAIN


Theoretical massNumber of molelcules
Total (without water)70,1424
Polymers70,1424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
crystal symmetry operation2_555-x,-y,z1
Buried area5700 Å2
ΔGint-33.3 kcal/mol
Surface area27920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.976, 104.922, 57.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-2113-

HOH

21A-2161-

HOH

31A-2209-

HOH

41A-2230-

HOH

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Components

#1: Protein DWV-VP3-P-DOMAIN


Mass: 17535.582 Da / Num. of mol.: 1 / Fragment: P-DOMAIN, RESIDUES 260-398
Source method: isolated from a genetically manipulated source
Details: PART OF THE VP3 CHAIN OF THE DEFORMED WING VIRUS. / Source: (gene. exp.) DEFORMED WING VIRUS / Plasmid: PET22T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8B3M2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE WILL BE UPLOAD SOON TO THE UNIPROT DATABASE.

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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: 3.16 Å3/Da / Density % sol: 61.09 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 4.3 M NACL,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2016
Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL
RadiationMonochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.45→39.75 Å / Num. obs: 34920 / % possible obs: 99.9 % / Observed criterion σ(I): 2.1 / Redundancy: 6.09 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.36 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.1 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→39.749 Å / SU ML: 0.17 / σ(F): 1.39 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 1754 5 %
Rwork0.1887 --
obs0.1899 34919 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→39.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 0 242 1484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061520
X-RAY DIFFRACTIONf_angle_d1.0472099
X-RAY DIFFRACTIONf_dihedral_angle_d13.247575
X-RAY DIFFRACTIONf_chiral_restr0.045205
X-RAY DIFFRACTIONf_plane_restr0.005291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48930.35611150.2592524X-RAY DIFFRACTION99
1.4893-1.53310.28841500.24732507X-RAY DIFFRACTION100
1.5331-1.58260.28451350.23382501X-RAY DIFFRACTION100
1.5826-1.63910.24561260.24012539X-RAY DIFFRACTION100
1.6391-1.70480.25651270.22192537X-RAY DIFFRACTION100
1.7048-1.78230.25161380.20992506X-RAY DIFFRACTION100
1.7823-1.87630.21231380.2022571X-RAY DIFFRACTION100
1.8763-1.99390.22771430.1992511X-RAY DIFFRACTION100
1.9939-2.14780.20541470.19662537X-RAY DIFFRACTION100
2.1478-2.36390.20261450.19522552X-RAY DIFFRACTION100
2.3639-2.70590.25641200.20252570X-RAY DIFFRACTION100
2.7059-3.40890.21191320.18382604X-RAY DIFFRACTION100
3.4089-39.76390.16841380.15662706X-RAY DIFFRACTION100

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