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

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Basic information

Entry
Database: PDB / ID: 6shl
TitleStructure of a marine algae virus of the order Picornavirales
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Picornavirales / Marnaviridae / icosahedral virus / algae virus / jelly roll
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsMunke, A. / Tomaru, Y. / Kimura, K. / Okamoto, K.
Funding support Sweden, 2items
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, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 4, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Apr 29, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Sep 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4


Theoretical massNumber of molelcules
Total (without water)89,5684
Polymers89,5684
Non-polymers00
Water0
1
A: VP1
B: VP2
C: VP3
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,374,066240
Polymers5,374,066240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation59

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Components

#1: Protein VP1


Mass: 29740.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros tenuissimus RNA virus type-II / References: UniProt: A0A0B6VJB4
#2: Protein VP2


Mass: 25911.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros tenuissimus RNA virus type-II / References: UniProt: A0A0B6VJB4
#3: Protein VP3


Mass: 28508.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros tenuissimus RNA virus type-II / References: UniProt: A0A0B6VJB4
#4: Protein VP4


Mass: 5406.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros tenuissimus RNA virus type-II / References: UniProt: A0A0B6VMZ2, UniProt: A0A0B6VJB4*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chaetoceros tenuissimus RNA virus type-II / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Chaetoceros tenuissimus RNA virus type-II
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Chaetoceros tenuissimus
Virus shellName: Capsid / Triangulation number (T number): 3
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 140000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 29 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2592
Image scansMovie frames/image: 32

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
4CTFFIND4CTF correction
7Coot0.8.9model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.15.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9920
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8315 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: BACKBONE TRACE / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0096466
ELECTRON MICROSCOPYf_angle_d1.18822
ELECTRON MICROSCOPYf_dihedral_angle_d8.3953796
ELECTRON MICROSCOPYf_chiral_restr0.066970
ELECTRON MICROSCOPYf_plane_restr0.0091159

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