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- PDB-5g52: Crystallographic structure of full particle of Deformed Wing Virus -

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Basic information

Entry
Database: PDB / ID: 5g52
TitleCrystallographic structure of full particle of Deformed Wing Virus
Components
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / PICORNAVIRALES / IFLAVIRIDAE / IFLAVIRUS / DWV CAPSID / P JELLYROLL / CATALYTIC SITE PROTEASE / LIPASE ESTERASE RECEPTO
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
URIDINE-5'-MONOPHOSPHATE / Genome polyprotein
Similarity search - Component
Biological speciesDEFORMED WING VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.802 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 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9364
Polymers99,6123
Non-polymers3241
Water00
1
A: VP1
B: VP2
C: VP3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,996,189240
Polymers5,976,738180
Non-polymers19,45160
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: VP1
B: VP2
C: VP3
hetero molecules
x 5


  • icosahedral pentamer
  • 500 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)499,68220
Polymers498,06115
Non-polymers1,6215
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 600 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)599,61924
Polymers597,67418
Non-polymers1,9456
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)360.131, 360.131, 360.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.309, 0.5, 0.809), (-0.5, 0.809, -0.309), (-0.809, -0.309, 0.5)
3generate(0.309, -0.5, 0.809), (0.5, 0.809, 0.309), (-0.809, 0.309, 0.5)
4generate(0.809, 0.309, 0.5), (0.309, 0.5, -0.809), (-0.5, 0.809, 0.309)
5generate(0.809, -0.309, 0.5), (-0.309, 0.5, 0.809), (-0.5, -0.809, 0.309)
6generate(0.5, 0.809, -0.309), (-0.809, 0.309, -0.5), (-0.309, 0.5, 0.809)
7generate(0.5, 0.809, 0.309), (-0.809, 0.309, 0.5), (0.309, -0.5, 0.809)
8generate(0.5, -0.809, -0.309), (0.809, 0.309, 0.5), (-0.309, -0.5, 0.809)
9generate(0.5, -0.809, 0.309), (0.809, 0.309, -0.5), (0.309, 0.5, 0.809)
10generate(0.809, -0.309, -0.5), (-0.309, 0.5, -0.809), (0.5, 0.809, 0.309)
11generate(0.809, 0.309, -0.5), (0.309, 0.5, 0.809), (0.5, -0.809, 0.309)
12generate(0.309, 0.5, -0.809), (-0.5, 0.809, 0.309), (0.809, 0.309, 0.5)
13generate(0.309, -0.5, -0.809), (0.5, 0.809, -0.309), (0.809, -0.309, 0.5)
14generate(-0.309, 0.5, 0.809), (0.5, 0.809, -0.309), (-0.809, 0.309, -0.5)
15generate(-0.309, -0.5, 0.809), (-0.5, 0.809, 0.309), (-0.809, -0.309, -0.5)
16generate(1), (-1), (-1)
17generate(1), (-1), (-1)
18generate(-1), (1), (-1)
19generate(1), (1), (1)
20generate(-0.5, 0.809, 0.309), (-0.809, -0.309, -0.5), (-0.309, -0.5, 0.809)
21generate(-0.5, -0.809, 0.309), (0.809, -0.309, 0.5), (-0.309, 0.5, 0.809)
22generate(0.809, 0.309, -0.5), (-0.309, -0.5, -0.809), (-0.5, 0.809, -0.309)
23generate(0.809, 0.309, 0.5), (-0.309, -0.5, 0.809), (0.5, -0.809, -0.309)
24generate(0.809, -0.309, -0.5), (0.309, -0.5, 0.809), (-0.5, -0.809, -0.309)
25generate(0.809, -0.309, 0.5), (0.309, -0.5, -0.809), (0.5, 0.809, -0.309)
26generate(-0.5, 0.809, -0.309), (-0.809, -0.309, 0.5), (0.309, 0.5, 0.809)
27generate(-0.5, -0.809, -0.309), (0.809, -0.309, -0.5), (0.309, -0.5, 0.809)
28generate(-1), (-1), (1)
29generate(1), (1), (1)
30generate(-1), (1), (-1)
31generate(-1), (-1), (1)
32generate(-0.309, -0.5, -0.809), (-0.5, 0.809, -0.309), (0.809, 0.309, -0.5)
33generate(-0.309, 0.5, -0.809), (0.5, 0.809, 0.309), (0.809, -0.309, -0.5)
34generate(-0.809, 0.309, 0.5), (-0.309, 0.5, -0.809), (-0.5, -0.809, -0.309)
35generate(-0.809, -0.309, 0.5), (0.309, 0.5, 0.809), (-0.5, 0.809, -0.309)
36generate(0.5, 0.809, 0.309), (0.809, -0.309, -0.5), (-0.309, 0.5, -0.809)
37generate(0.5, -0.809, 0.309), (-0.809, -0.309, 0.5), (-0.309, -0.5, -0.809)
38generate(-0.309, 0.5, -0.809), (-0.5, -0.809, -0.309), (-0.809, 0.309, 0.5)
39generate(-0.309, 0.5, 0.809), (-0.5, -0.809, 0.309), (0.809, -0.309, 0.5)
40generate(-0.309, -0.5, -0.809), (0.5, -0.809, 0.309), (-0.809, -0.309, 0.5)
41generate(-0.309, -0.5, 0.809), (0.5, -0.809, -0.309), (0.809, 0.309, 0.5)
42generate(0.5, -0.809, -0.309), (-0.809, -0.309, -0.5), (0.309, 0.5, -0.809)
43generate(0.5, 0.809, -0.309), (0.809, -0.309, 0.5), (0.309, -0.5, -0.809)
44generate(-0.809, 0.309, -0.5), (-0.309, 0.5, 0.809), (0.5, 0.809, -0.309)
45generate(-0.809, -0.309, -0.5), (0.309, 0.5, -0.809), (0.5, -0.809, -0.309)
46generate(-1), (1), (-1)
47generate(-0.5, 0.809, -0.309), (0.809, 0.309, -0.5), (-0.309, -0.5, -0.809)
48generate(-0.5, -0.809, 0.309), (-0.809, 0.309, -0.5), (0.309, -0.5, -0.809)
49generate(-0.5, -0.809, -0.309), (-0.809, 0.309, 0.5), (-0.309, 0.5, -0.809)
50generate(-0.5, 0.809, 0.309), (0.809, 0.309, 0.5), (0.309, 0.5, -0.809)
51generate(-0.809, 0.309, -0.5), (0.309, -0.5, -0.809), (-0.5, -0.809, 0.309)
52generate(-0.809, -0.309, 0.5), (-0.309, -0.5, -0.809), (0.5, -0.809, 0.309)
53generate(-0.809, -0.309, -0.5), (-0.309, -0.5, 0.809), (-0.5, 0.809, 0.309)
54generate(-0.809, 0.309, 0.5), (0.309, -0.5, 0.809), (0.5, 0.809, 0.309)
55generate(0.309, 0.5, -0.809), (0.5, -0.809, -0.309), (-0.809, -0.309, -0.5)
56generate(0.309, -0.5, 0.809), (-0.5, -0.809, -0.309), (0.809, -0.309, -0.5)
57generate(0.309, -0.5, -0.809), (-0.5, -0.809, 0.309), (-0.809, 0.309, -0.5)
58generate(0.309, 0.5, 0.809), (0.5, -0.809, 0.309), (0.809, 0.309, -0.5)
59generate(1), (-1), (-1)
60generate(-1), (-1), (1)

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Components

#1: Protein VP1


Mass: 27123.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEFORMED WING VIRUS / References: UniProt: Q8B3M2*PLUS
#2: Protein VP2


Mass: 28005.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEFORMED WING VIRUS / References: UniProt: Q8B3M2*PLUS
#3: Protein VP3


Mass: 44483.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) DEFORMED WING VIRUS / References: UniProt: Q8B3M2*PLUS
#4: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P
Sequence detailsSEQUENCE TO THE UNIPROT WILL BE UPLOAD SOON.

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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

CrystalDescription: MODEL WAS USED FROM CRYOEM RECONSTRUCTION
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.8 M POTASSIUM DIHYDROGEN PHOSPHATE, 0.8 M SODIUM DIHYDROGEN PHOSPHATE, 0.1 M SODIUM HEPES, 7.5 PH

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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
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: 3.8→29.8 Å / Num. obs: 56889 / % possible obs: 75.7 % / Observed criterion σ(I): 0.9 / Redundancy: 1.8 % / Rmerge(I) obs: 0.37 / Net I/σ(I): 2
Reflection shellResolution: 3.8→3.91 Å / Redundancy: 1.78 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 0.9 / % possible all: 76.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.802→29.805 Å / SU ML: 0.68 / σ(F): 1.36 / Phase error: 34.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3224 2844 5 %
Rwork0.2828 --
obs0.2849 56873 75.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.802→29.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7025 0 20 0 7045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836215
X-RAY DIFFRACTIONf_angle_d1.46649380
X-RAY DIFFRACTIONf_dihedral_angle_d16.21513010
X-RAY DIFFRACTIONf_chiral_restr0.0555355
X-RAY DIFFRACTIONf_plane_restr0.0066385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8016-3.8670.40541430.35652673X-RAY DIFFRACTION75
3.867-3.93720.3491310.34452732X-RAY DIFFRACTION77
3.9372-4.01270.37041540.32912697X-RAY DIFFRACTION76
4.0127-4.09440.34851300.3172700X-RAY DIFFRACTION75
4.0944-4.18320.35751440.31482743X-RAY DIFFRACTION76
4.1832-4.28030.32831460.30682720X-RAY DIFFRACTION76
4.2803-4.3870.29431510.28932733X-RAY DIFFRACTION76
4.387-4.50520.31591330.27382769X-RAY DIFFRACTION78
4.5052-4.63730.30691510.27832702X-RAY DIFFRACTION76
4.6373-4.78640.33021500.27182777X-RAY DIFFRACTION77
4.7864-4.95670.32851330.26852764X-RAY DIFFRACTION77
4.9567-5.15420.31671400.27092727X-RAY DIFFRACTION76
5.1542-5.38750.31350.2712750X-RAY DIFFRACTION76
5.3875-5.66970.35191440.26782701X-RAY DIFFRACTION75
5.6697-6.02220.34731430.28882712X-RAY DIFFRACTION76
6.0222-6.48280.29241490.27152757X-RAY DIFFRACTION77
6.4828-7.12710.29331590.26532731X-RAY DIFFRACTION75
7.1271-8.140.28361290.24642641X-RAY DIFFRACTION73
8.14-10.1870.24811310.21922583X-RAY DIFFRACTION71
10.187-29.80560.32551480.25782417X-RAY DIFFRACTION66

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