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- EMDB-4115: Israeli acute paralysis virus heated to 63 degree - empty particle -

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Basic information

Entry
Database: EMDB / ID: EMD-4115
TitleIsraeli acute paralysis virus heated to 63 degree - empty particle
Map data
Sample
  • Virus: Israeli acute paralysis virus
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: Structural polyprotein
KeywordsIAPV / Dicistroviridae / empty particle / Virus
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Capsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesIsraeli acute paralysis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMullapudi E / Fuzik T
Funding support Czech Republic, Germany, 2 items
OrganizationGrant numberCountry
European Research Counciln. 355855 Czech Republic
European Molecular Biology Organization#3041 Germany
CitationJournal: J Virol / Year: 2017
Title: Cryo-electron Microscopy Study of the Genome Release of the Dicistrovirus Israeli Acute Bee Paralysis Virus.
Authors: Edukondalu Mullapudi / Tibor Füzik / Antonín Přidal / Pavel Plevka /
Abstract: Viruses of the family Dicistroviridae can cause substantial economic damage by infecting agriculturally important insects. Israeli acute bee paralysis virus (IAPV) causes honeybee colony collapse ...Viruses of the family Dicistroviridae can cause substantial economic damage by infecting agriculturally important insects. Israeli acute bee paralysis virus (IAPV) causes honeybee colony collapse disorder in the United States. High-resolution molecular details of the genome delivery mechanism of dicistroviruses are unknown. Here we present a cryo-electron microscopy analysis of IAPV virions induced to release their genomes in vitro We determined structures of full IAPV virions primed to release their genomes to a resolution of 3.3 Å and of empty capsids to a resolution of 3.9 Å. We show that IAPV does not form expanded A particles before genome release as in the case of related enteroviruses of the family Picornaviridae The structural changes observed in the empty IAPV particles include detachment of the VP4 minor capsid proteins from the inner face of the capsid and partial loss of the structure of the N-terminal arms of the VP2 capsid proteins. Unlike the case for many picornaviruses, the empty particles of IAPV are not expanded relative to the native virions and do not contain pores in their capsids that might serve as channels for genome release. Therefore, rearrangement of a unique region of the capsid is probably required for IAPV genome release.
IMPORTANCE: Honeybee populations in Europe and North America are declining due to pressure from pathogens, including viruses. Israeli acute bee paralysis virus (IAPV), a member of the family ...IMPORTANCE: Honeybee populations in Europe and North America are declining due to pressure from pathogens, including viruses. Israeli acute bee paralysis virus (IAPV), a member of the family Dicistroviridae, causes honeybee colony collapse disorder in the United States. The delivery of virus genomes into host cells is necessary for the initiation of infection. Here we present a structural cryo-electron microscopy analysis of IAPV particles induced to release their genomes. We show that genome release is not preceded by an expansion of IAPV virions as in the case of related picornaviruses that infect vertebrates. Furthermore, minor capsid proteins detach from the capsid upon genome release. The genome leaves behind empty particles that have compact protein shells.
History
DepositionOct 11, 2016-
Header (metadata) releaseOct 19, 2016-
Map releaseNov 30, 2016-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5lwi
  • Surface level: 3.4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5lwi
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4115.png

Downloads & links

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Map

FileDownload / File: emd_4115.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
1.07 Å/pix.
x 330 pix.
= 353.1 Å		1.07 Å/pix.
x 330 pix.
= 353.1 Å		1.07 Å/pix.
x 330 pix.
= 353.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.4 / Movie #1: 3.4
Minimum - Maximum-7.2490635 - 11.736589
Average (Standard dev.)-0.00000000281475 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-165-165-165
Dimensions330330330
Spacing330330330
CellA=B=C: 353.1 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z353.100353.100353.100
α/β/γ90.00090.00090.000
start NX/NY/NZ-165-165-165
NX/NY/NZ330330330
MAP C/R/S312
start NC/NR/NS-165-165-165
NC/NR/NS330330330
D min/max/mean-7.24911.737-0.000

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Supplemental data

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Sample components

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Entire : Israeli acute paralysis virus

EntireName: Israeli acute paralysis virus
Components
  • Virus: Israeli acute paralysis virus
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: Structural polyprotein

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Supramolecule #1: Israeli acute paralysis virus

SupramoleculeName: Israeli acute paralysis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 294365 / Sci species name: Israeli acute paralysis virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Apis mellifera (honey bee)

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Israeli acute paralysis virus
Molecular weightTheoretical: 23.776541 KDa
SequenceString: INIGNKTNEN VISFFDSTDA ETQNHNALMK GCGEFIVNLR TLLRTFRTIT DNWILQANTK TPITDLTNTT DAQGRDYMSY LSYLYRFYR GGRRYKFFNT TPLKQSQTCY IRSFLIPRNY SADEINVDGP SHITYPVINP VHEVEVPFYS QYRKIPIAST S DKGYDSSL ...String:
INIGNKTNEN VISFFDSTDA ETQNHNALMK GCGEFIVNLR TLLRTFRTIT DNWILQANTK TPITDLTNTT DAQGRDYMSY LSYLYRFYR GGRRYKFFNT TPLKQSQTCY IRSFLIPRNY SADEINVDGP SHITYPVINP VHEVEVPFYS QYRKIPIAST S DKGYDSSL MYFSNTATTQ IVARAGNDDF TFGWMIGPPQ LQGESRSVAP

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Israeli acute paralysis virus
Molecular weightTheoretical: 33.260754 KDa
SequenceString: SKPRNQQQVC PLQNVPAWGY SLYKGIDMSV PLAYDPNNEL GDLKDVFPSA VDEMAIGYVC GNPAVKHVLT WKTTDAIQKP IANGDDWGG VIPVGMPCYS KSIRTTRISA TENRETEVMD AAPCEYVANM FSYWRATMCY RITVVKTAFH TGRLEIFFEP G VIPVKPTV ...String:
SKPRNQQQVC PLQNVPAWGY SLYKGIDMSV PLAYDPNNEL GDLKDVFPSA VDEMAIGYVC GNPAVKHVLT WKTTDAIQKP IANGDDWGG VIPVGMPCYS KSIRTTRISA TENRETEVMD AAPCEYVANM FSYWRATMCY RITVVKTAFH TGRLEIFFEP G VIPVKPTV NNIGPDQDRL TGAVAPSDNN YKYILDLTND TEVTIRVPFV SNKMFLKTAG IYGANSENNW NFHESFSGFL CI RPVTKLM APDTVSDNVS IVVWKWAEDV VVVEPKPLTS GPTQVYRPPP TASTAVEVLN VEL

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Macromolecule #3: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Israeli acute paralysis virus
Molecular weightTheoretical: 26.482732 KDa
SequenceString: SENSVETQEI TTFHDVETPN RIDTPMAQDT SSARNMDDTH SIIQFLQRPV LIDNIEIIAG TTADANKPLS RYVLDQQNSQ KYVRSWTLP STVLRAGGKA QKLANFKYLR CDVQVKLVLN ANPFVAGRMY LAYSPYDDKV DTARSVLQTS RAGVTGYPGV E LDFQLDNS ...String:
SENSVETQEI TTFHDVETPN RIDTPMAQDT SSARNMDDTH SIIQFLQRPV LIDNIEIIAG TTADANKPLS RYVLDQQNSQ KYVRSWTLP STVLRAGGKA QKLANFKYLR CDVQVKLVLN ANPFVAGRMY LAYSPYDDKV DTARSVLQTS RAGVTGYPGV E LDFQLDNS VEMTIPYASF QEAYDLVTGT EDFVQLYLFP ITPVLGPKSE SESSKVDISV YMWLSNISLV IPTYRINP

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 1500 / Average exposure time: 1.0 sec. / Average electron dose: 21.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Detailsmovie frames were drift aligned by Spider package
Startup modelType of model: OTHER
Details: density map of crystall structure of pdb:5CDC was used as initial model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Software - details: relion_refine (autorefine) / Number images used: 1138
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) / Software - details: relion_refine (autorefine) / Details: relion_refine (autorefine)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) / Software - details: relion_refine (autorefine) / Details: relion_refine (autorefine)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 1.4) / Software - details: relion_refine / Details: regularization factor = 4
FSC plot (resolution estimation)

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Atomic model buiding 1

Detailsinitial rigid body fit was done by Chimera, then the model was refined using realspace refinement in Phenix and finaly reciprocal refined in REFMAC.
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT
Output model

PDB-5lwi:
Israeli acute paralysis virus heated to 63 degree - empty particle

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