[English] 日本語
Yorodumi
- EMDB-12558: Virion of Leishmania RNA virus 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12558
TitleVirion of Leishmania RNA virus 1
Map dataNative virion of Leishmania RNA virus 1
Sample
  • Virus: Leishmania RNA virus 1
    • Protein or peptide: Capsid proteinCapsid
Function / homologyTotivirus coat / Totivirus coat protein / Capsid protein
Function and homology information
Biological speciesLeishmania RNA virus 1 - LgM5313 / Leishmania RNA virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsProchazkova M / Grybchuk D / Fuzik T
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic20-22689S Czech Republic
Citation
Journal: Virology / Year: 2022
Title: Virion structure of Leishmania RNA virus 1.
Authors: Michaela Procházková / Tibor Füzik / Danyil Grybchuk / Vyacheslav Yurchenko / Pavel Plevka /
Abstract: The presence of Leishmania RNA virus 1 (LRV1) enables Leishmania protozoan parasites to cause more severe disease than the virus-free strains. The structure of LRV1 virus-like particles has been ...The presence of Leishmania RNA virus 1 (LRV1) enables Leishmania protozoan parasites to cause more severe disease than the virus-free strains. The structure of LRV1 virus-like particles has been determined previously, however, the structure of the LRV1 virion has not been characterized. Here we used cryo-electron microscopy and single-particle reconstruction to determine the structures of the LRV1 virion and empty particle isolated from Leishmania guyanensis to resolutions of 4.0 Å and 3.6 Å, respectively. The capsid of LRV1 is built from sixty dimers of capsid proteins organized with icosahedral symmetry. RNA genomes of totiviruses are replicated inside the virions by RNA polymerases expressed as C-terminal extensions of a sub-population of capsid proteins. Most of the virions probably contain one or two copies of the RNA polymerase, however, the location of the polymerase domains in LRV1 capsid could not be identified, indicating that it varies among particles. Importance. Every year over 200 000 people contract leishmaniasis and more than five hundred people die of the disease. The mucocutaneous form of leishmaniasis produces lesions that can destroy the mucous membranes of the nose, mouth, and throat. Leishmania parasites carrying Leishmania RNA virus 1 (LRV1) are predisposed to cause aggravated symptoms in the mucocutaneous form of leishmaniasis. Here, we present the structure of the LRV1 virion determined using cryo-electron microscopy.
#1: Journal: J Virol / Year: 2021
Title: Capsid Structure of Leishmania RNA virus 1
Authors: Prochazkova M / Fuzik T / Grybchuk D / Falginella FL / Podesvova L / Yurchenko V / Vacha R / Plevka P
History
DepositionMar 5, 2021-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_12558.png

Downloads & links

-
Map

FileDownload / File: emd_12558.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNative virion of Leishmania RNA virus 1
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.034988288 - 0.073103175
Average (Standard dev.)0.0013036424 (±0.0055915997)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 482.40002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Leishmania RNA virus 1

EntireName: Leishmania RNA virus 1
Components
  • Virus: Leishmania RNA virus 1
    • Protein or peptide: Capsid proteinCapsid

-
Supramolecule #1: Leishmania RNA virus 1

SupramoleculeName: Leishmania RNA virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1678905 / Sci species name: Leishmania RNA virus 1 / Sci species strain: 1-4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Leishmania guyanensis (eukaryote) / Strain: MHOM/BR/75/M4147
Molecular weightTheoretical: 9.1 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 421.0 Å / T number (triangulation number): 2

-
Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania RNA virus 1 - LgM5313
Molecular weightTheoretical: 86.431742 KDa
SequenceString: MADIPNSDKI ACGRKPMFCE IIKLANRKRL IFNTTDERVY DARLNYCSTA DSTVQADCHI YWRLKLRRTD AVFEEYTGQG YSLDTAAYP QQYTDIIRGY YSKHVSSSLA ANTQHFVNVL AMLRHAGACI AHYCMTGKID FDILSKKKHK NKEVVTLSNA D SLSFLPHS ...String:
MADIPNSDKI ACGRKPMFCE IIKLANRKRL IFNTTDERVY DARLNYCSTA DSTVQADCHI YWRLKLRRTD AVFEEYTGQG YSLDTAAYP QQYTDIIRGY YSKHVSSSLA ANTQHFVNVL AMLRHAGACI AHYCMTGKID FDILSKKKHK NKEVVTLSNA D SLSFLPHS ALYLPSPLRA SDPEIFNMLY LLGCACDASI AMDNISNTSG AAKYSMPHYN PLQLSHALHV TIFYMLSLMD SC GYGDDAV LALTSGLHSV TTVIAHSDEG GITRDALREL SYTQPYGTMP VPIAGYFQHI NVLFTTQPAW DQFAGIWDYV ILA TAALVH LSDPGMTVND VTYPTTLTTK VATVDGRNSD LAAQMMHSAT RFCDIFVENL STFWGVVANP DGNASQALLH AFNI VACAV EPNRHLEMNV MAPWYWVESS ALFCDYAPFR SPISSAGYGP QCVYGARLVL AATNSLEFTG EAGDYSAYRF EWTTM RHNP LFNILNKRVG DGLANVDFRL RPFNEWLLEG QPSRRSCNSA GHGTPTATCS HKTPNHDTLD EYIWGSTSCD LFHPAE LTS YTAVCVRFRN YLSGADGDVR ILNTPTREVI EGNVVTRCDG IRCLDSNKRI QHVPEVARRY CMMARYLAQA RTFGALT IG DDIIRGFDKV EKIVKMHKSN NRLDQMPLID VTGLCQPMIE TSTVRASTTT RIDPNKLAAA TARVELPLAP RCTSSLIP S SDTVPEPEPQ VGEPGDNGGC APDLGTGGGS GIEGRGSMDI GDPNSVQALA RLQASSVDKL AAALE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration15 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMHEPESHEPES
150.0 mMNaClSodium chloridesodium chloride

Details: pH 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK II
DetailsBuffer: 50 mM HEPES pH 7.4, 150 mM NaCl

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 3981 / Average electron dose: 1.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 7912
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: EMDB MAP
EMDB ID:

10722

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.7) / Number images used: 3768
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6y83


Chain - Chain ID: A
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 72.61 / Target criteria: correlation coefficient
Output model

PDB-7ns2:
Virion of Leishmania RNA virus 1

+
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