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- PDB-5lsf: Sacbrood honeybee virus -

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Basic information

Entry
Database: PDB / ID: 5lsf
TitleSacbrood honeybee virus
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Iflaviridae / external VP4
Function / homology
Function and homology information


RNA-protein covalent cross-linking / host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / membrane => GO:0016020 / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription ...RNA-protein covalent cross-linking / host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / membrane => GO:0016020 / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 ...Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Polyprotein / Polyprotein / Structural polyprotein / Structural protein Vp1 / Genome polyprotein
Similarity search - Component
Biological speciesSacbrood virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPlevka, P. / Veselikova, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Republic
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Virion structure and genome delivery mechanism of sacbrood honeybee virus.
Authors: Michaela Procházková / Tibor Füzik / Karel Škubník / Jana Moravcová / Zorica Ubiparip / Antonín Přidal / Pavel Plevka /
Abstract: Infection by sacbrood virus (SBV) from the family Iflaviridae is lethal to honey bee larvae but only rarely causes the collapse of honey bee colonies. Despite the negative effect of SBV on honey ...Infection by sacbrood virus (SBV) from the family Iflaviridae is lethal to honey bee larvae but only rarely causes the collapse of honey bee colonies. Despite the negative effect of SBV on honey bees, the structure of its particles and mechanism of its genome delivery are unknown. Here we present the crystal structure of SBV virion and show that it contains 60 copies of a minor capsid protein (MiCP) attached to the virion surface. No similar MiCPs have been previously reported in any of the related viruses from the order Picornavirales. The location of the MiCP coding sequence within the SBV genome indicates that the MiCP evolved from a C-terminal extension of a major capsid protein by the introduction of a cleavage site for a virus protease. The exposure of SBV to acidic pH, which the virus likely encounters during cell entry, induces the formation of pores at threefold and fivefold axes of the capsid that are 7 Å and 12 Å in diameter, respectively. This is in contrast to vertebrate picornaviruses, in which the pores along twofold icosahedral symmetry axes are currently considered the most likely sites for genome release. SBV virions lack VP4 subunits that facilitate the genome delivery of many related dicistroviruses and picornaviruses. MiCP subunits induce liposome disruption in vitro, indicating that they are functional analogs of VP4 subunits and enable the virus genome to escape across the endosome membrane into the cell cytoplasm.
History
DepositionAug 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5016
Polymers88,4214
Non-polymers802
Water7,512417
1
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,310,079360
Polymers5,305,270240
Non-polymers4,809120
Water4,324240
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
D: VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 443 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)442,50730
Polymers442,10620
Non-polymers40110
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 531 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)531,00836
Polymers530,52724
Non-polymers48112
Water43224
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)487.850, 360.970, 338.160
Angle α, β, γ (deg.)90.000, 133.070, 90.000
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.429185, -0.549563, 0.716745), (0.059337, 0.809, 0.584774), (-0.901254, -0.208474, 0.379815)
3generate(0.429185, 0.549563, 0.716745), (-0.059337, 0.809, -0.584774), (-0.901254, 0.208474, 0.379815)
4generate(0.49438, 0.453587, 0.741504), (-0.829887, 0.5, 0.247487), (-0.258496, -0.737713, 0.62362)
5generate(0.49438, -0.453587, 0.741504), (0.829887, 0.5, -0.247487), (-0.258496, 0.737713, 0.62362)
6generate(0.992934, -0.095977, -0.069379), (0.095977, 0.309, 0.946187), (-0.069379, -0.946187, 0.316066)
7generate(0.395936, -0.889224, -0.22912), (0.889224, 0.309, 0.337287), (-0.22912, -0.337287, 0.913064)
8generate(0.992934, 0.095977, -0.069379), (-0.095977, 0.309, -0.946187), (-0.069379, 0.946187, 0.316066)
9generate(0.395936, 0.889224, -0.22912), (-0.889224, 0.309, -0.337287), (-0.22912, 0.337287, 0.913064)
10generate(0.494379, 0.829887, -0.258496), (-0.453587, 0.5, 0.737713), (0.741504, -0.247487, 0.62362)
11generate(0.494379, -0.829887, -0.258496), (0.453587, 0.5, -0.737713), (0.741504, 0.247487, 0.62362)
12generate(0.429185, -0.059337, -0.901254), (0.549563, 0.809, 0.208474), (0.716745, -0.584774, 0.379815)
13generate(0.429185, 0.059337, -0.901254), (-0.549563, 0.809, -0.208474), (0.716745, 0.584774, 0.379815)
14generate(-0.429185, -0.059337, 0.901254), (-0.549563, 0.809, -0.208474), (-0.716745, -0.584774, -0.379815)
15generate(-0.429185, 0.059337, 0.901254), (0.549563, 0.809, 0.208474), (-0.716745, 0.584774, -0.379815)
16generate(0.483008, -0.6089, 0.629241), (-0.793247, 0.6089), (-0.370759, -0.793247, -0.483008)
17generate(-0.483008, -0.793247, 0.370759), (0.6089, 0.793247), (-0.629241, 0.6089, 0.483008)
18generate(0.483008, 0.6089, 0.629241), (0.793247, -0.6089), (-0.370759, 0.793247, -0.483008)
19generate(-0.483008, 0.793247, 0.370759), (-0.6089, -0.793247), (-0.629241, -0.6089, 0.483008)
20generate(0.323676, -0.889224, -0.323258), (0.095977, -0.309, 0.946187), (-0.941257, -0.337287, -0.014676)
21generate(0.323676, 0.889224, -0.323258), (-0.095977, -0.309, -0.946187), (-0.941257, 0.337287, -0.014676)
22generate(0.588517, 0.453587, 0.669244), (-0.453587, -0.5, 0.737713), (0.669244, -0.737713, -0.088517)
23generate(-0.377499, -0.829887, 0.410762), (0.829887, -0.5, -0.247487), (0.410762, 0.247487, 0.877499)
24generate(0.588517, -0.453587, 0.669244), (0.453587, -0.5, -0.737713), (0.669244, 0.737713, -0.088517)
25generate(-0.377499, 0.829887, 0.410762), (-0.829887, -0.5, 0.247487), (0.410762, -0.247487, 0.877499)
26generate(0.323676, -0.095977, -0.941257), (0.889224, -0.309, 0.337287), (-0.323258, -0.946187, -0.014676)
27generate(0.323676, 0.095977, -0.941257), (-0.889224, -0.309, -0.337287), (-0.323258, 0.946187, -0.014676)
28generate(0.483008, 0.793247, -0.370759), (0.6089, 0.793247), (0.629241, -0.6089, -0.483008)
29generate(-0.483008, -0.6089, -0.629241), (0.793247, -0.6089), (0.370759, -0.793247, 0.483008)
30generate(0.483008, -0.793247, -0.370759), (-0.6089, -0.793247), (0.629241, 0.6089, -0.483008)
31generate(-0.483008, 0.6089, -0.629241), (-0.793247, 0.6089), (0.370759, 0.793247, 0.483008)
32generate(-0.429185, 0.549563, -0.716745), (0.059337, 0.809, 0.584774), (0.901254, 0.208474, -0.379815)
33generate(-0.429185, -0.549563, -0.716745), (-0.059337, 0.809, -0.584774), (0.901254, -0.208474, -0.379815)
34generate(-0.494379, -0.829887, 0.258496), (-0.453587, 0.5, 0.737713), (-0.741504, 0.247487, -0.62362)
35generate(-0.494379, 0.829887, 0.258496), (0.453587, 0.5, -0.737713), (-0.741504, -0.247487, -0.62362)
36generate(-0.323676, -0.095977, 0.941257), (-0.889224, -0.309, -0.337287), (0.323258, -0.946187, 0.014676)
37generate(-0.323676, 0.095977, 0.941257), (0.889224, -0.309, 0.337287), (0.323258, 0.946187, 0.014676)
38generate(0.981563, -0.059337, -0.181642), (0.059337, -0.809, 0.584774), (-0.181642, -0.584774, -0.790563)
39generate(-0.581451, -0.549563, -0.599865), (0.549563, -0.809, 0.208474), (-0.599865, -0.208474, 0.772451)
40generate(0.981563, 0.059337, -0.181642), (-0.059337, -0.809, -0.584774), (-0.181642, 0.584774, -0.790563)
41generate(-0.581451, 0.549563, -0.599865), (-0.549563, -0.809, -0.208474), (-0.599865, 0.208474, 0.772451)
42generate(-0.323676, 0.889224, 0.323258), (0.095977, -0.309, 0.946187), (0.941257, 0.337287, 0.014676)
43generate(-0.323676, -0.889224, 0.323258), (-0.095977, -0.309, -0.946187), (0.941257, -0.337287, 0.014676)
44generate(-0.49438, 0.453587, -0.741504), (0.829887, 0.5, -0.247487), (0.258496, -0.737713, -0.62362)
45generate(-0.49438, -0.453587, -0.741504), (-0.829887, 0.5, 0.247487), (0.258496, 0.737713, -0.62362)
46generate(-1), (1), (-1)
47generate(-0.395936, -0.889224, 0.22912), (-0.889224, 0.309, -0.337287), (0.22912, -0.337287, -0.913064)
48generate(-0.992934, 0.095977, 0.069379), (0.095977, 0.309, 0.946187), (0.069379, 0.946187, -0.316066)
49generate(-0.395936, 0.889224, 0.22912), (0.889224, 0.309, 0.337287), (0.22912, 0.337287, -0.913064)
50generate(-0.992934, -0.095977, 0.069379), (-0.095977, 0.309, -0.946187), (0.069379, -0.946187, -0.316066)
51generate(0.377499, -0.829887, -0.410762), (-0.829887, -0.5, 0.247487), (-0.410762, 0.247487, -0.877499)
52generate(-0.588517, -0.453587, -0.669244), (-0.453587, -0.5, 0.737713), (-0.669244, 0.737713, 0.088517)
53generate(0.377499, 0.829887, -0.410762), (0.829887, -0.5, -0.247487), (-0.410762, -0.247487, -0.877499)
54generate(-0.588517, 0.453587, -0.669244), (0.453587, -0.5, -0.737713), (-0.669244, -0.737713, 0.088517)
55generate(0.581451, -0.549563, 0.599865), (-0.549563, -0.809, -0.208474), (0.599865, -0.208474, -0.772451)
56generate(-0.981563, 0.059337, 0.181642), (0.059337, -0.809, 0.584774), (0.181642, 0.584774, 0.790563)
57generate(0.581451, 0.549563, 0.599865), (0.549563, -0.809, 0.208474), (0.599865, 0.208474, -0.772451)
58generate(-0.981563, -0.059337, 0.181642), (-0.059337, -0.809, -0.584774), (0.181642, -0.584774, 0.790563)
59generate(-0.258482, 0.966016), (-1), (0.966016, 0.258482)
60generate(0.258482, -0.966016), (-1), (-0.966016, -0.258482)

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein VP1


Mass: 27659.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sacbrood virus / References: UniProt: Q9WCE9
#2: Protein VP2


Mass: 26952.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sacbrood virus / References: UniProt: Q6ITS8, UniProt: A0A2S0CUG6*PLUS
#3: Protein VP3


Mass: 30701.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sacbrood virus / References: UniProt: I1U3P9, UniProt: A0A2S0CUG6*PLUS

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide VP4


Mass: 3107.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sacbrood virus / References: UniProt: Q9IGK7, UniProt: A0A2S0CUG6*PLUS

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Non-polymers , 2 types, 419 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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

Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG4000, isopropanol, magnesium chloride, MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 1572113 / % possible obs: 64 % / Redundancy: 3.1 % / CC1/2: 0.977 / Rmerge(I) obs: 0.135 / Net I/σ(I): 6.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1 / % possible all: 21.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
CNSrefinement
PDB_EXTRACT3.2data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1b35

1b35


Resolution: 2.1→50 Å / Cross valid method: NONE / σ(F): 0
Details: Viral structure with icosahedral symmetry, we did not use R-free.
RfactorNum. reflection% reflection
Rwork0.1939 --
obs-1572113 63.6 %
Solvent computationBsol: 39.6553 Å2
Displacement parametersBiso max: 73.26 Å2 / Biso mean: 25.3479 Å2 / Biso min: 12.11 Å2
Baniso -1Baniso -2Baniso -3
1--4.437 Å20 Å2-1.74 Å2
2---0.24 Å2-0 Å2
3---4.677 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6230 0 2 417 6649
Biso mean--61.27 32.83 -
Num. residues----781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.44
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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