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- PDB-5j98: Crystal structure of Slow Bee Paralysis Virus at 2.6A resolution -

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Basic information

Entry
Database: PDB / ID: 5j98
TitleCrystal structure of Slow Bee Paralysis Virus at 2.6A resolution
Components
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / icosahedral virus / honeybee / protrusion
Function / homology
Function and homology information


host cell membrane / viral capsid / RNA helicase activity / 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 / Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 ...Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Jelly Rolls - #20 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Jelly Rolls / 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 / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSlow bee paralysis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKalynych, S. / Levdansky, Y. / Palkova, L. / Plevka, P.
CitationJournal: J.Virol. / Year: 2016
Title: Virion Structure of Iflavirus Slow Bee Paralysis Virus at 2.6-Angstrom Resolution.
Authors: Kalynych, S. / Pridal, A. / Palkova, L. / Levdansky, Y. / de Miranda, J.R. / Plevka, P.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3


Theoretical massNumber of molelcules
Total (without water)107,7553
Polymers107,7553
Non-polymers00
Water1,24369
1
A: VP1
B: VP2
C: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)6,465,320180
Polymers6,465,320180
Non-polymers00
Water3,243180
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
x 5


  • icosahedral pentamer
  • 539 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)538,77715
Polymers538,77715
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
x 6


  • icosahedral 23 hexamer
  • 647 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)646,53218
Polymers646,53218
Non-polymers00
Water32418
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)340.042, 396.848, 431.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I60 (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5)
3generate(0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017)
4generate(0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017)
5generate(0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5)
6generate(-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017)
7generate(-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017)
8generate(0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017)
9generate(0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017)
10generate(1), (-1), (-1)
11generate(0.309017, -0.809017, 0.5), (-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017)
12generate(0.5, 0.309017, 0.809017), (-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017)
13generate(1), (1), (1)
14generate(-0.5, 0.309017, -0.809017), (-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017)
15generate(-0.309017, -0.809017, -0.5), (-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017)
16generate(-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017), (0.309017, 0.809017, -0.5)
17generate(-1), (1), (-1)
18generate(-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017), (0.309017, -0.809017, -0.5)
19generate(-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5), (0.809017, -0.5, 0.309017)
20generate(-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017)
21generate(0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5)
22generate(0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017)
23generate(-1), (1), (-1)
24generate(0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017)
25generate(0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5)
26generate(-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5), (0.809017, -0.5, -0.309017)
27generate(-1), (-1), (1)
28generate(0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5), (0.809017, 0.5, -0.309017)
29generate(0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017), (0.5, 0.309017, -0.809017)
30generate(-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017), (0.5, -0.309017, -0.809017)
31generate(-1), (1), (-1)
32generate(0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017)
33generate(0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017)
34generate(-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017)
35generate(-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017)
36generate(-0.309017, 0.809017, 0.5), (-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017)
37generate(-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5)
38generate(-0.809017, -0.5, -0.309017), (-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5)
39generate(-0.309017, -0.809017, 0.5), (-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017)
40generate(1), (-1), (-1)
41generate(0.809017, 0.5, -0.309017), (0.5, -0.309017, 0.809017), (0.309017, -0.809017, -0.5)
42generate(0.5, 0.309017, -0.809017), (0.309017, 0.809017, 0.5), (0.809017, -0.5, 0.309017)
43generate(0.5, -0.309017, -0.809017), (-0.309017, 0.809017, -0.5), (0.809017, 0.5, 0.309017)
44generate(0.809017, -0.5, -0.309017), (-0.5, -0.309017, -0.809017), (0.309017, 0.809017, -0.5)
45generate(1), (-1), (-1)
46generate(-1), (-1), (1)
47generate(0.309017, -0.809017, -0.5), (-0.809017, -0.5, 0.309017), (-0.5, 0.309017, -0.809017)
48generate(0.809017, -0.5, 0.309017), (-0.5, -0.309017, 0.809017), (-0.309017, -0.809017, -0.5)
49generate(0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017), (0.309017, -0.809017, 0.5)
50generate(0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017)
51generate(-0.309017, -0.809017, 0.5), (0.809017, -0.5, -0.309017), (0.5, 0.309017, 0.809017)
52generate(1), (1), (1)
53generate(-0.309017, 0.809017, 0.5), (0.809017, 0.5, -0.309017), (-0.5, 0.309017, -0.809017)
54generate(-0.809017, 0.5, -0.309017), (0.5, 0.309017, -0.809017), (-0.309017, -0.809017, -0.5)
55generate(-0.809017, -0.5, -0.309017), (0.5, -0.309017, -0.809017), (0.309017, -0.809017, 0.5)
56generate(-0.5, 0.309017, 0.809017), (-0.309017, 0.809017, -0.5), (-0.809017, -0.5, -0.309017)
57generate(-0.809017, 0.5, 0.309017), (-0.5, -0.309017, -0.809017), (-0.309017, -0.809017, 0.5)
58generate(-1), (-1), (1)
59generate(-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5)
60generate(-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5), (-0.809017, 0.5, -0.309017)

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Components

#1: Protein VP1


Mass: 30307.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Slow bee paralysis virus / References: UniProt: A7LM73
#2: Protein VP2


Mass: 29824.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Slow bee paralysis virus / References: UniProt: A7LM73
#3: Protein VP3


Mass: 47623.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Slow bee paralysis virus / References: UniProt: A7LM73
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: rhomboid long bars measuring as long as 300 micrometers in the longest dimension
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: Sodium acetate pH 4.5, 5% (v/v) PEG-10,000 / PH range: 4.5-5.5 / Temp details: 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.6→49.5 Å / Num. obs: 780730 / % possible obs: 88.3 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 0.9 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 0.9 / % possible all: 69.3

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Processing

Software
NameVersionClassification
CNS1.3refinement
PHENIXrefinement
XDSaidata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J96

5j96


Resolution: 2.6→49.5 Å / Cross valid method: NONE /
RfactorNum. reflection% reflection
obs0.279 780730 88.3 %
Refinement stepCycle: LAST / Resolution: 2.6→49.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7369 0 0 69 7438
Refine LS restraintsType: NCS

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