[English] 日本語
Yorodumi
- EMDB-3863: Sacbrood virus of honeybee -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3863
TitleSacbrood virus of honeybee
Map data
Sample
  • Virus: Sacbrood virus
    • Protein or peptide: structural protein VP1Structure
    • Protein or peptide: structural protein VP2Structure
    • Protein or peptide: structural protein VP3Structure
    • Protein or peptide: minor capsid protein MiCP
Function / homology
Function and homology information


RNA-protein covalent cross-linking / host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity ...RNA-protein covalent cross-linking / host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / 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
Genome polyprotein / Genome polyprotein / Structural polyprotein / Structural protein Vp1 / Genome polyprotein
Similarity search - Component
Biological speciesSacbrood virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsPlevka P / Prochazkova M
Funding support Czech Republic, 2 items
OrganizationGrant numberCountry
European Research CouncilFP/2007-2013 (355855) Czech Republic
European Molecular Biology OrganizationIG-3041 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
DepositionSep 11, 2017-
Header (metadata) releaseNov 29, 2017-
Map releaseJul 18, 2018-
UpdateNov 13, 2019-
Current statusNov 13, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5oyp
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5oyp
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3863.png

Downloads & links

-
Map

FileDownload / File: emd_3863.map.gz / Format: CCP4 / Size: 620.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.063 Å
Density
Contour LevelBy EMDB: 4.0 / Movie #1: 4
Minimum - Maximum-11.506444 - 22.413900000000002
Average (Standard dev.)-0.000000000494095 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-273-273-273
Dimensions546546546
Spacing546546546
CellA=B=C: 580.398 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS-273-273-273
NC/NR/NS546546546
D min/max/mean-11.50622.414-0.000

-
Supplemental data

-
Additional map: #1

Fileemd_3863_additional.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Sacbrood virus

EntireName: Sacbrood virus
Components
  • Virus: Sacbrood virus
    • Protein or peptide: structural protein VP1Structure
    • Protein or peptide: structural protein VP2Structure
    • Protein or peptide: structural protein VP3Structure
    • Protein or peptide: minor capsid protein MiCP

-
Supramolecule #1: Sacbrood virus

SupramoleculeName: Sacbrood virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 89463 / Sci species name: Sacbrood virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Apis mellifera (honey bee)
Host systemOrganism: Apis mellifera (honey bee)
Virus shellShell ID: 1 / Name: capsid / Diameter: 271.3 Å / T number (triangulation number): 3

-
Macromolecule #1: structural protein VP1

MacromoleculeName: structural protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sacbrood virus
Molecular weightTheoretical: 27.659998 KDa
Recombinant expressionOrganism: Apis mellifera (honey bee)
SequenceString: MDTGAKEDED ETANFSDGVT AMGFQSLDTQ VSIKDILRRP VLLFNHVELD PDYTGFFIPI MPPSRMMQYK SGDKETSFQR LIGRTPQAA IMNLFRFWRG SLRYTIIIHS TDGHPIYVTH VPHTGNRVYG LMKVNNLHEY TKVPIFGCGL TTEMIIPSVN P SICVEVPF ...String:
MDTGAKEDED ETANFSDGVT AMGFQSLDTQ VSIKDILRRP VLLFNHVELD PDYTGFFIPI MPPSRMMQYK SGDKETSFQR LIGRTPQAA IMNLFRFWRG SLRYTIIIHS TDGHPIYVTH VPHTGNRVYG LMKVNNLHEY TKVPIFGCGL TTEMIIPSVN P SICVEVPF DTENNWAVTF DEDAQRNYSW RDKGDTVTGH LVVTPVVSVY MSVWVEAGDD FEVSNFYGPP SVKTNDWNYA FS DEH

-
Macromolecule #2: structural protein VP2

MacromoleculeName: structural protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sacbrood virus
Molecular weightTheoretical: 26.952393 KDa
Recombinant expressionOrganism: Apis mellifera (honey bee)
SequenceString: EVPSKESIQG DATQQSSKEE NTIITRDQQQ TVSENIPSTV GDLVIASSEP TQQFRSLTNR WMPINSIRVT VNGKRNDLLA QYYIPEDFL STHAKCAPNT IPFETYVYGK YELEMKFVAN GNKFQCGKVI ISVKFDSYQA DNINTGFQAA LSRPHIMLDL S TNNEGVLK ...String:
EVPSKESIQG DATQQSSKEE NTIITRDQQQ TVSENIPSTV GDLVIASSEP TQQFRSLTNR WMPINSIRVT VNGKRNDLLA QYYIPEDFL STHAKCAPNT IPFETYVYGK YELEMKFVAN GNKFQCGKVI ISVKFDSYQA DNINTGFQAA LSRPHIMLDL S TNNEGVLK IPFRYHRAFV RNQTHKTATA GVRPGKFASI YVQVLSPLQT GEGGANDMFI RPFYRYTRAE FAGMSYKVPL T

-
Macromolecule #3: structural protein VP3

MacromoleculeName: structural protein VP3 / type: protein_or_peptide / ID: 3 / Details: Genbank id KY617033d / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sacbrood virus
Molecular weightTheoretical: 30.701373 KDa
Recombinant expressionOrganism: Apis mellifera (honey bee)
SequenceString: DKPKDVSSIT IIPKPRLGFP HGKGKSDAVA MRVNPVALTS FQDVSAYPDE PRTTLDIARI WGLRSTFNWG SGDEHGKELF NTVLDPGLR FYDQDYEGQI TPMEYVTGLY NFWSGPIELR FDFVSNAFHT GTVIISAEYN RSSTNTDECQ SHSTYTKTFH L GEQKSVHF ...String:
DKPKDVSSIT IIPKPRLGFP HGKGKSDAVA MRVNPVALTS FQDVSAYPDE PRTTLDIARI WGLRSTFNWG SGDEHGKELF NTVLDPGLR FYDQDYEGQI TPMEYVTGLY NFWSGPIELR FDFVSNAFHT GTVIISAEYN RSSTNTDECQ SHSTYTKTFH L GEQKSVHF TVPYIYDTVV RRNTASAYLP VTDYDKVDNV SRAQAMGIRA ESKMRVKVRV VNVLRPVAST TSTIEVLVYM RG GKNYALH GLKQSTYWPS NSVVPIDSFP PDGYDP

-
Macromolecule #4: minor capsid protein MiCP

MacromoleculeName: minor capsid protein MiCP / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sacbrood virus
Molecular weightTheoretical: 3.107398 KDa
Recombinant expressionOrganism: Apis mellifera (honey bee)
SequenceString:
DNPHRFLPAN VSNRWNEYSS AYLPRV

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration15 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium chloridesodium chloride
2.7 mMKClpotassium chloride
10.0 mMNa2HPO4disodium phosphate
1.8 mMKH2PO4potassium phosphate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 74325 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
DetailsPreliminar grid screening was performed manually on FEI Tecnai F20 (cryo stage).
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 2-16 / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 21.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 31804
Details: Full virions were selected together with empty particles from the same set of micrographs. Subsequent 2D classification sorted the particles of two types. Full and empty particles were ...Details: Full virions were selected together with empty particles from the same set of micrographs. Subsequent 2D classification sorted the particles of two types. Full and empty particles were further reconstructed separately.
CTF correctionSoftware - Name: Gctf / Software - details: Dr. Kai Zhang
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5cdc


Details: Deposited IAPV model low pass filtered to resolution 40 A.
Initial angle assignmentType: OTHER
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2) / Details: re-classification after initial 3D refinement
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2) / Software - details: relion_refine_mpi
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 10303
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 53.85 / Target criteria: R-factor
Output model

PDB-5oyp:
Sacbrood virus of honeybee

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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