[English] 日本語
Yorodumi
- EMDB-12173: KBV activated particle at acidic pH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12173
TitleKBV activated particle at acidic pH
Map dataKBV activated particle at acidic pH
Sample
  • Virus: Kashmir bee virus
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
KeywordsViruses / Riboviria / Orthornavirae / Pisuviricota / Pisoniviricetes / Picornavirales / Dicistroviridae / Aparavirus / Kashmir Bee Virus / 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
Similarity search - Component
Biological speciesKashmir bee virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMukhamedova L / Plevka P
Funding support Czech Republic, 2 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
Ministry of Education (MoE, Czech Republic)LM2011033 Czech Republic
CitationJournal: J Virol / Year: 2021
Title: Virion structure and genome release mechanism of dicistrovirus Kashmir bee virus.
Authors: Liya Mukhamedova / Tibor Füzik / Jiří Nováček / Dominik Hrebík / Antonín Přidal / Gerardo A Marti / Diego M A Guérin / Pavel Plevka /
Abstract: Infections of Kashmir bee virus (KBV) are lethal for honeybees and have been associated with colony collapse disorder. KBV and closely related viruses contribute to the ongoing decline in the number ...Infections of Kashmir bee virus (KBV) are lethal for honeybees and have been associated with colony collapse disorder. KBV and closely related viruses contribute to the ongoing decline in the number of honeybee colonies in North America, Europe, Australia, and other parts of the world. Despite the economic and ecological impact of KBV, its structure and infection process remain unknown. Here we present the structure of the virion of KBV determined to a resolution of 2.8 Å. We show that the exposure of KBV to acidic pH induces a reduction in inter-pentamer contacts within capsids and the reorganization of its RNA genome from a uniform distribution to regions of high and low density. Capsids of KBV crack into pieces at acidic pH, resulting in the formation of open particles lacking pentamers of capsid proteins. The large openings of capsids enable the rapid release of genomes and thus limit the probability of their degradation by RNases. The opening of capsids may be a shared mechanism for the genome release of viruses from the family The western honeybee () is indispensable for maintaining agricultural productivity as well as the abundance and diversity of wild flowering plants. However, bees suffer from environmental pollution, parasites, and pathogens, including viruses. Outbreaks of virus infections cause the deaths of individual honeybees as well as collapses of whole colonies. Kashmir bee virus has been associated with colony collapse disorder in the US, and no cure of the disease is currently available. Here we report the structure of an infectious particle of Kashmir bee virus and show how its protein capsid opens to release the genome. Our structural characterization of the infection process determined that therapeutic compounds stabilizing contacts between pentamers of capsid proteins could prevent the genome release of the virus.
History
DepositionJan 6, 2021-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7bg8
  • Surface level: 0.019
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bg8
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12173.png

Downloads & links

-
Map

FileDownload / File: emd_12173.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKBV activated particle at acidic pH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 340 pix.
= 363.8 Å		1.07 Å/pix.
x 340 pix.
= 363.8 Å		1.07 Å/pix.
x 340 pix.
= 363.8 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: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.05562485 - 0.0706761
Average (Standard dev.)0.00023101317 (±0.0068516955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-170-170-170
Dimensions340340340
Spacing340340340
CellA=B=C: 363.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z363.800363.800363.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-170-170-170
NC/NR/NS340340340
D min/max/mean-0.0560.0710.000

-
Supplemental data

-
Sample components

-
Entire : Kashmir bee virus

EntireName: Kashmir bee virus
Components
  • Virus: Kashmir bee virus
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein

-
Supramolecule #1: Kashmir bee virus

SupramoleculeName: Kashmir bee virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 68876 / Sci species name: Kashmir bee virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Apis mellifera (honey bee)
Molecular weightTheoretical: 5.932 MDa
Virus shellShell ID: 1 / Name: Full virus / Diameter: 350.0 Å / T number (triangulation number): 3

-
Macromolecule #1: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kashmir bee virus
Molecular weightTheoretical: 23.807529 KDa
SequenceString: INLSNKTDEN TISFFDSGDP ERMNNEALMR GCGEQIVNLR PLLRTFRTIN DNWSLAANTK TPITDLTNTA DAEGRDYMSY LSFLYRFYR GGRRYKFFNT TPLKQSQTCY VRSFLIPRNY TADEINTDGP SHITYPVINP VHEVEVPFYS QYRKIPIAST S DKGYDSSL ...String:
INLSNKTDEN TISFFDSGDP ERMNNEALMR GCGEQIVNLR PLLRTFRTIN DNWSLAANTK TPITDLTNTA DAEGRDYMSY LSFLYRFYR GGRRYKFFNT TPLKQSQTCY VRSFLIPRNY TADEINTDGP SHITYPVINP VHEVEVPFYS QYRKIPIAST S DKGYDSSL MYYTNVGTQQ IVARAGNDDF TFGWMIGTPQ LQGITKEVAN

UniProtKB: Structural polyprotein

-
Macromolecule #2: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kashmir bee virus
Molecular weightTheoretical: 33.335781 KDa
SequenceString: SKPRNQNQVM PYQNVPGWGY SLYKGIDMSV PLAYDPNNEL GDLRDVFPSA VDEMAIGYVC GNPAIKHVLT WSTTDVVQNP ISNGDDWGG VIPVGMPCYS KTIRAVKGAT STSKTEVMDP APCEYVANLF SYWRATMCYR ITVVKTAFHT GRLEIFFEPG S IPTVRTAD ...String:
SKPRNQNQVM PYQNVPGWGY SLYKGIDMSV PLAYDPNNEL GDLRDVFPSA VDEMAIGYVC GNPAIKHVLT WSTTDVVQNP ISNGDDWGG VIPVGMPCYS KTIRAVKGAT STSKTEVMDP APCEYVANLF SYWRATMCYR ITVVKTAFHT GRLEIFFEPG S IPTVRTAD NLGPDQTQLN GTIAPSDNNY KYILDLTNDT EVTIKVPYVS NKMFMKTVGI YGAHDEDNWN FDESFTGFLC IR PITKLMA PDTVSQKVSI VVWKWAEDVV VVEPKPLTSG PTQVYNPPAV ARDLVKQIDV SMQ

UniProtKB: Structural polyprotein

-
Macromolecule #3: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kashmir bee virus
Molecular weightTheoretical: 34.750039 KDa
SequenceString: ADNQENDSTN VHNTKLASTS AENAIEKEQI TTFHDVETPN RIDTPMAQDT SSARSMDDTH SIIQFLQRPV LIDNIEIVAG TTADNNTAL SRYVLDRTNP QKYIKQWTLP STVLKAGGKA QKLANFKYLR CDVQVKIVLN ANPFIAGRLY LAYSPYDDKV A PERRIIYT ...String:
ADNQENDSTN VHNTKLASTS AENAIEKEQI TTFHDVETPN RIDTPMAQDT SSARSMDDTH SIIQFLQRPV LIDNIEIVAG TTADNNTAL SRYVLDRTNP QKYIKQWTLP STVLKAGGKA QKLANFKYLR CDVQVKIVLN ANPFIAGRLY LAYSPYDDKV A PERRIIYT SRAGVTGYPG VELDFQLDNS VEMTIPYASF QEAYDLVSGN EDFVQLYLFT IAPVLGPSAE SANSKVDLSV YM WLDNISL VIPTYRLNPN LPTGQTLTRI VQNSDSDKLK EALKIAKSKN PSGYKYIMGV LEQYNPSVKQ VSMQ

UniProtKB: Structural polyprotein

-
Macromolecule #4: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kashmir bee virus
Molecular weightTheoretical: 7.066156 KDa
SequenceString:
IATPNKSKST KPTSENPKIG PISEVASGVK TAANGIERIP VLGEIAKPVT AAVKWFADIV GGVAAIFGW

UniProtKB: Structural polyprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 6
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 103.15 K / Max: 108.15 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 8193 / Average exposure time: 1.0 sec. / Average electron dose: 94.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 4.134 µm / Calibrated defocus min: 0.214 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.2 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

+
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4115

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Details: I4 symmetry implemented. / Number images used: 794
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5cdc


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 45.18 / Target criteria: Cross- correlation
Output model

PDB-7bg8:
KBV activated particle at acidic pH

+
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