6SHL

Structure of a marine algae virus of the order Picornavirales


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Capsid structure of a marine algae virus of the order Picornavirales.

Munke, A.Kimura, K.Tomaru, Y.Okamoto, K.

(2020) J.Virol. --: --

  • DOI: 10.1128/JVI.01855-19

  • PubMed Abstract: 
  • The order <i>Picornavirales </i> 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 cer ...

    The order Picornavirales 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 Picornavirales ancestor in some respects. Herein, we present the capsid structure of Chaetoceros tenuissimus RNA virus type II (CtenRNAV-II) determined using cryo-electron microscopy at a resolution of 3.1 Å, the first of an algae virus belonging to the family Marnaviridae of the order Picornavirales 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, that another VP1 loop obscures the so-called canyon, which is a host-receptor binding site for many of the mammalian Picornavirales viruses. VP2 has an N-terminal tail, which has previously been reported as a primordial feature of Picornavirales viruses. Based on the above-mentioned and other critical structural features, the acquired traits among Picornavirales viruses were categorized for profound discussions. The observations afford new insights on three long-standing theories among Picornavirales : the canyon hypothesis, the primordial VP2 domain swap, and the hypothesis that algae picorna-like viruses could share characteristics with the Picornavirales ancestor. Importance Identifying the acquired structural traits in virus capsids is important for elucidating what functions are essential among viruses that infect different hosts. The Picornavirales 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 Picornavirales ancestor. This manuscript describes the first atomic capsid structure of an alga Marnavirus, 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 Picornavirales viruses.


    Organizational Affiliation

    The Laboratory of Molecular Biophysics, Department of Cell and Molecular biology, Uppsala University, Sweden kenta.okamoto@icm.uu.se.,National Research Institute of Fisheries and Environment of Inland Sea, Japan Fisheries Research and Education Agency, Japan.,Department of Biological Resource Science, Faculty of Agriculture, Saga University, Japan.,The Laboratory of Molecular Biophysics, Department of Cell and Molecular biology, Uppsala University, Sweden anna.munke@icm.uu.se.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A
267Chaetoceros tenuissimus RNA virus type-IIMutation(s): 0 
Find proteins for A0A0B6VJB4 (Chaetoceros tenuissimus RNA virus type-II)
Go to UniProtKB:  A0A0B6VJB4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP2
B
231Chaetoceros tenuissimus RNA virus type-IIMutation(s): 0 
Find proteins for A0A0B6VJB4 (Chaetoceros tenuissimus RNA virus type-II)
Go to UniProtKB:  A0A0B6VJB4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP3
C
262Chaetoceros tenuissimus RNA virus type-IIMutation(s): 0 
Find proteins for A0A0B6VJB4 (Chaetoceros tenuissimus RNA virus type-II)
Go to UniProtKB:  A0A0B6VJB4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
VP4
D
51Chaetoceros tenuissimus RNA virus type-IIMutation(s): 0 
Find proteins for A0A0B6VMZ2 (Chaetoceros tenuissimus RNA virus type-II)
Go to UniProtKB:  A0A0B6VMZ2
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2018-03387
Swedish Research CouncilSweden2018-00421

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release
  • Version 1.1: 2020-02-19
    Type: Database references