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- EMDB-10200: Structure of a marine algae virus of the order Picornavirales -

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Basic information

Entry
Database: EMDB / ID: EMD-10200
TitleStructure of a marine algae virus of the order Picornavirales
Map data
Sample
  • Virus: Chaetoceros tenuissimus RNA virus type-II
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
Function / homologyCapsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Predicted structural protein / Predicted structural protein
Function and homology information
Biological speciesChaetoceros tenuissimus RNA virus type-II
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMunke A / Tomaru Y / Kimura K / Okamoto K
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research Council2018-03387 Sweden
Swedish Research Council2018-00421 Sweden
CitationJournal: J Virol / Year: 2020
Title: Capsid Structure of a Marine Algal Virus of the Order .
Authors: Anna Munke / Kei Kimura / Yuji Tomaru / Kenta Okamoto /
Abstract: The order includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as ...The order includes viruses that infect different kinds of eukaryotes and that share similar properties. The capsid proteins (CPs) of viruses in the order that infect unicellular organisms, such as algae, presumably possess certain characteristics that have changed little over the course of evolution, and thus these viruses may resemble the ancestor in some respects. Herein, we present the capsid structure of RNA virus type II (CtenRNAV-II) determined using cryo-electron microscopy at a resolution of 3.1 Å, the first alga virus belonging to the family of the order A structural comparison to related invertebrate and vertebrate viruses revealed a unique surface loop of the major CP VP1 that had not been observed previously, and further, revealed that another VP1 loop obscures the so-called canyon, which is a host-receptor binding site for many of the mammalian viruses. VP2 has an N-terminal tail, which has previously been reported as a primordial feature of viruses. The above-mentioned and other critical structural features provide new insights on three long-standing theories about : (i) the canyon hypothesis, (ii) the primordial VP2 domain swap, and (iii) the hypothesis that alga viruses could share characteristics with the ancestor. Identifying the acquired structural traits in virus capsids is important for elucidating what functions are essential among viruses that infect different hosts. The viruses infect a broad spectrum of hosts, ranging from unicellular algae to insects and mammals and include many human pathogens. Those viruses that infect unicellular protists, such as algae, are likely to have undergone fewer structural changes during the course of evolution compared to those viruses that infect multicellular eukaryotes and thus still share some characteristics with the ancestor. This article describes the first atomic capsid structure of an alga , CtenRNAV-II. A comparison to capsid structures of the related invertebrate and vertebrate viruses identified a number of structural traits that have been functionally acquired or lost during the course of evolution. These observations provide new insights on past theories on the viability and evolution of viruses.
History
DepositionAug 7, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseFeb 12, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.127
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6shl
  • Surface level: 0.127
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6shl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10200.png

Downloads & links

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Map

FileDownload / File: emd_10200.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.127 / Movie #1: 0.127
Minimum - Maximum-0.273615 - 0.464667
Average (Standard dev.)0.0029608626 (±0.027028225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 476.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z477.000477.000477.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.2740.4650.003

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Supplemental data

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Sample components

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Entire : Chaetoceros tenuissimus RNA virus type-II

EntireName: Chaetoceros tenuissimus RNA virus type-II
Components
  • Virus: Chaetoceros tenuissimus RNA virus type-II
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4

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Supramolecule #1: Chaetoceros tenuissimus RNA virus type-II

SupramoleculeName: Chaetoceros tenuissimus RNA virus type-II / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1516128 / Sci species name: Chaetoceros tenuissimus RNA virus type-II / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Chaetoceros tenuissimus (Diatom)
Virus shellShell ID: 1 / Name: Capsid / T number (triangulation number): 3

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros tenuissimus RNA virus type-II
Molecular weightTheoretical: 29.740906 KDa
SequenceString: DNSNNPVGGN PIDNYGTEHA PLLKEDNQYL VYQGERIVSF KDLLRRYQYL NSYWPQETGS GFRYYTLDSP GMPIYRGWDP NGIDQGQDS TAGNSPYNFC SMTLLNYLAP AFVCQRGSLR HKWVTAGARV NSTASVLSAT RHGVLFPLPL AETAHPLDNA L VGDRRSEL ...String:
DNSNNPVGGN PIDNYGTEHA PLLKEDNQYL VYQGERIVSF KDLLRRYQYL NSYWPQETGS GFRYYTLDSP GMPIYRGWDP NGIDQGQDS TAGNSPYNFC SMTLLNYLAP AFVCQRGSLR HKWVTAGARV NSTASVLSAT RHGVLFPLPL AETAHPLDNA L VGDRRSEL QEMQRSRLNG TAITPVRLNN TLEIELPYYS IGQRFHASRF LDLAGTGDTQ GVEIACEISD GGNDANYRLD QF VSVGEDF TLGMFVGAPI MYFYNDPTAT

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros tenuissimus RNA virus type-II
Molecular weightTheoretical: 25.911801 KDa
SequenceString: PSANDGPSFT TSKTSQNTTS ENVHFVDGDT PWTYDVAATP DETSKLSGFD DAGLGEFLSR PIKIQQYQWT PGVQLFQTFN PWSDYFGNA DVLEKINRFR NLRCKLCLKV LINGNSFYYG RALLSYNPYL RNDQVTVNRS FFIQDLIAAS NKPHILLDPC S SEGGQMCL ...String:
PSANDGPSFT TSKTSQNTTS ENVHFVDGDT PWTYDVAATP DETSKLSGFD DAGLGEFLSR PIKIQQYQWT PGVQLFQTFN PWSDYFGNA DVLEKINRFR NLRCKLCLKV LINGNSFYYG RALLSYNPYL RNDQVTVNRS FFIQDLIAAS NKPHILLDPC S SEGGQMCL PFIWPENYLD ITSTGWEDQM GECIIHDFDV LRHANGGTDP ITVSIFAWAE DVSLLIPTTV AAQ

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros tenuissimus RNA virus type-II
Molecular weightTheoretical: 28.508686 KDa
SequenceString: SRPAVLSDIQ PYVPRYCGNL ANSDAPETVN KLSVDSKNEL TIDTRTMGLG GADELTIHSI ASRMTFWRQF DWPESAVTDT LLASMSVQP FCIDTVTASP VTEIHSTALA FASAPFETWQ GSIKFHFKVV CSEYHRGRLR LVYNPLTNNA GPVAFNQVYS T TIDISNDR ...String:
SRPAVLSDIQ PYVPRYCGNL ANSDAPETVN KLSVDSKNEL TIDTRTMGLG GADELTIHSI ASRMTFWRQF DWPESAVTDT LLASMSVQP FCIDTVTASP VTEIHSTALA FASAPFETWQ GSIKFHFKVV CSEYHRGRLR LVYNPLTNNA GPVAFNQVYS T TIDISNDR EFDYECKWTD IRAWNACIGI DGATSATFFN TAAAVTGGTP FDNGTLSVYV VNELATPSTA AADVKVQVWV SA GDDFAVA VPGVGLSQLS YFQQQ

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros tenuissimus RNA virus type-II
Molecular weightTheoretical: 5.406366 KDa
SequenceString:
EFKHDGLISK PASAVAKAAD ALSMIPYIAP YAKATSMVAD KIGKIARIFG Y

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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

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 140000
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: COUNTING / Number grids imaged: 1 / Number real images: 2592 / Average exposure time: 8.0 sec. / Average electron dose: 29.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9920
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 8315
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6shl:
Structure of a marine algae virus of the order Picornavirales

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