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- EMDB-10722: Capsid structure of Leishmania RNA virus 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-10722
TitleCapsid structure of Leishmania RNA virus 1
Map dataMap rotated to crystallographic orientation with origin in 000.
SampleLeishmania RNA virus 1 - 4 != Leishmania RNA virus 1 - LgM5313

Leishmania RNA virus 1 - 4

  • Virus: Leishmania RNA virus 1 - LgM5313
    • Protein or peptide: Capsid protein
Keywordsvirus-like particle / capsid structure / VIRUS LIKE PARTICLE
Function / homologyTotivirus coat / Totivirus coat protein / Capsid protein
Function and homology information
Biological speciesLeishmania RNA virus 1 - 4 / Leishmania RNA virus 1 - LgM5313
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsProchazkova M / Fuzik T
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
European Research Council (ERC) Czech Republic
CitationJournal: J Virol / Year: 2021
Title: Capsid Structure of RNA Virus 1.
Authors: Michaela Procházková / Tibor Füzik / Danyil Grybchuk / Francesco Luca Falginella / Lucie Podešvová / Vyacheslav Yurchenko / Robert Vácha / Pavel Plevka /
Abstract: parasites cause a variety of symptoms, including mucocutaneous leishmaniasis, which results in the destruction of the mucous membranes of the nose, mouth, and throat. The species of carrying RNA ... parasites cause a variety of symptoms, including mucocutaneous leishmaniasis, which results in the destruction of the mucous membranes of the nose, mouth, and throat. The species of carrying RNA virus 1 (LRV1), from the family , are more likely to cause severe disease and are less sensitive to treatment than those that do not contain the virus. Although the importance of LRV1 for the severity of leishmaniasis was discovered a long time ago, the structure of the virus remained unknown. Here, we present a cryo-electron microscopy reconstruction of the virus-like particle of LRV1 determined to a resolution of 3.65 Å. The capsid has icosahedral symmetry and is formed by 120 copies of a capsid protein assembled in asymmetric dimers. RNA genomes of viruses from the family are synthetized, but not capped at the 5' end, by virus RNA polymerases. To protect viral RNAs from degradation, capsid proteins of the L-A totivirus cleave the 5' caps of host mRNAs, creating decoys to overload the cellular RNA quality control system. Capsid proteins of LRV1 form positively charged clefts, which may be the cleavage sites for the 5' cap of mRNAs. The putative RNA binding site of LRV1 is distinct from that of the related L-A virus. The structure of the LRV1 capsid enables the rational design of compounds targeting the putative decapping site. Such inhibitors may be developed into a treatment for mucocutaneous leishmaniasis caused by LRV1-positive species of Twelve million people worldwide suffer from leishmaniasis, resulting in more than 30 thousand deaths annually. The disease has several variants that differ in their symptoms. The mucocutaneous form, which leads to disintegration of the nasal septum, lips, and palate, is caused predominantly by parasites carrying RNA virus 1 (LRV1). Here, we present the structure of the LRV1 capsid determined using cryo-electron microscopy. Capsid proteins of a related totivirus, L-A virus, protect viral RNAs from degradation by cleaving the 5' caps of host mRNAs. Capsid proteins of LRV1 may have the same function. We show that the LRV1 capsid contains positively charged clefts that may be sites for the cleavage of mRNAs of cells. The structure of the LRV1 capsid enables the rational design of compounds targeting the putative mRNA cleavage site. Such inhibitors may be used as treatments for mucocutaneous leishmaniasis.
History
DepositionMar 3, 2020-
Header (metadata) releaseNov 11, 2020-
Map releaseNov 11, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
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  • Surface view colored by radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6y83
  • Surface level: 0.05
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6y83
  • Imaged by Jmol
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Structure viewerEM map:
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Supplemental images

emd_10722.png

Downloads & links

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Map

FileDownload / File: emd_10722.map.gz / Format: CCP4 / Size: 620.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap rotated to crystallographic orientation with origin in 000.
Projections & slices

Image control

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

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.0893611 - 0.18737605
Average (Standard dev.)0.0021453528 (±0.011328808)
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-0.0890.1870.002

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Supplemental data

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Mask #1

Fileemd_10722_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map in original position, matches mask.

Fileemd_10722_additional_1.map
AnnotationMap in original position, matches mask.
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Leishmania RNA virus 1 - 4

EntireName: Leishmania RNA virus 1 - 4
Components
  • Virus: Leishmania RNA virus 1 - LgM5313
    • Protein or peptide: Capsid protein

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Supramolecule #1: Leishmania RNA virus 1 - LgM5313

SupramoleculeName: Leishmania RNA virus 1 - LgM5313 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1285422 / Sci species name: Leishmania RNA virus 1 - LgM5313 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Leishmania guyanensis (eukaryote) / Strain: MHOM/BR/75/M4147
Virus shellShell ID: 1 / Name: capsid / Diameter: 422.0 Å / T number (triangulation number): 2

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1
Details: Subunit A model for residues 15-204, 210-520, 541-635. Subunit B model for residues 19-290, 300-517, 541-576, 583-642.,Subunit A model for residues 15-204, 210-520, 541-635. Subunit B model ...Details: Subunit A model for residues 15-204, 210-520, 541-635. Subunit B model for residues 19-290, 300-517, 541-576, 583-642.,Subunit A model for residues 15-204, 210-520, 541-635. Subunit B model for residues 19-290, 300-517, 541-576, 583-642.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Leishmania RNA virus 1 - 4
Molecular weightTheoretical: 87.53693 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 AAALEHHHHH HHH

UniProtKB: Capsid protein

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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

Concentration15 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
50.0 mMTris
1.0 mMEDTA
5.0 mMB-mebetamercaptoethanol
GridModel: Quantifoil R2/1 / 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: 70 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK II / Details: blot force 3 blot time 5 wait time 10.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 12000 / Average exposure time: 0.5 sec. / Average electron dose: 21.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.0005 µm / Nominal defocus min: -0.0005 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

Particle selectionNumber selected: 28000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1m1c


Details: Initial model constructed.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 16901
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 1.8 degrees
Software - Name: RELION
Final 3D classificationNumber classes: 3 / Avg.num./class: 20000 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1m1c


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 174 / Target criteria: R-factor
Output model

PDB-6y83:
Capsid structure of Leishmania RNA virus 1

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