[English] 日本語
Yorodumi
- EMDB-3867: Sacbrood virus of honeybee - expansion state II -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3867
TitleSacbrood virus of honeybee - expansion state II
Map data
SampleSacbrood virus:
virus / (structural protein ...Protein) x 3 / minor capsid protein MiCP
Function / homologyPeptidase S1, PA clan / RNA helicase / 3C cysteine protease (picornain 3C) / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, catalytic domain / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus ...Peptidase S1, PA clan / RNA helicase / 3C cysteine protease (picornain 3C) / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, catalytic domain / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / RdRp of positive ssRNA viruses catalytic domain profile. / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA dependent RNA polymerase / RNA helicase activity / viral capsid / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / RNA binding / integral component of membrane / ATP binding / Genome polyprotein / Genome polyprotein / Structural protein Vp1
Function and homology information
SourceSacbrood virus
Methodsingle particle reconstruction / cryo EM / 7.25 Å resolution
AuthorsPlevka P / Prochazkova M
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.
Validation ReportPDB-ID: 6eh1

SummaryFull reportAbout validation report
DateDeposition: Sep 12, 2017 / Header (metadata) release: Oct 18, 2017 / Map release: Jul 18, 2018 / Last update: Oct 17, 2018

-
Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6eh1
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6eh1
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_3867.map.gz (map file in CCP4 format, 651086 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
546 pix
1.06 Å/pix.
= 580.398 Å
546 pix
1.06 Å/pix.
= 580.398 Å
546 pix
1.06 Å/pix.
= 580.398 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density
Contour Level:4.5 (by emdb), 0.04 (movie #1):
Minimum - Maximum-0.12586766 - 0.21891223
Average (Standard dev.)0.0012369186 (0.010741303)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions546546546
Origin-273.0-273.0-273.0
Limit272.0272.0272.0
Spacing546546546
CellA=B=C: 580.398 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z546546546
origin x/y/z0.0000.0000.000
length x/y/z580.398580.398580.398
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-273-273-273
NC/NR/NS546546546
D min/max/mean-0.1260.2190.001

-
Supplemental data

-
Sample components

+
Entire Sacbrood virus

EntireName: Sacbrood virus / Details: Isolated from honeybee pupae / Number of components: 5

+
Component #1: virus, Sacbrood virus

VirusName: Sacbrood virus / Class: VIRION / Details: Isolated from honeybee pupae / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Sacbrood virus
Source (natural)Host Species: Apis mellifera (honey bee)
Shell #1Name of element: capsid / Diameter: 278.86 Å / T number(triangulation number): 3

+
Component #2: protein, structural protein VP1

ProteinName: structural protein VP1Structure / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.27948 kDa
SourceSpecies: Sacbrood virus

+
Component #3: protein, structural protein VP2

ProteinName: structural protein VP2Structure / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.360314 kDa
SourceSpecies: Sacbrood virus

+
Component #4: protein, structural protein VP3

ProteinName: structural protein VP3Structure / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.574461 kDa
SourceSpecies: Sacbrood virus

+
Component #5: protein, minor capsid protein MiCP

ProteinName: minor capsid protein MiCP / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.107398 kDa
SourceSpecies: Sacbrood virus

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 15 mg/ml / pH: 5.8
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 70 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Details: Preliminar grid screening was performed manually on FEI Tecnai F20 (cryo stage).
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 21 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal), 74325.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 4000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 5330
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 7.25 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL / Overall bvalue: 268.70999999999998
Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more