6F2S

CryoEM structure of Ageratum Yellow Vein virus (AYVV)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The 3.3 angstrom structure of a plant geminivirus using cryo-EM.

Hesketh, E.L.Saunders, K.Fisher, C.Potze, J.Stanley, J.Lomonossoff, G.P.Ranson, N.A.

(2018) Nat Commun 9: 2369-2369

  • DOI: https://doi.org/10.1038/s41467-018-04793-6
  • Primary Citation of Related Structures:  
    6F2S

  • PubMed Abstract: 

    Geminiviruses are major plant pathogens that threaten food security globally. They have a unique architecture built from two incomplete icosahedral particles, fused to form a geminate capsid. However, despite their importance to agricultural economies and fundamental biological interest, the details of how this is realized in 3D remain unknown. Here we report the structure of Ageratum yellow vein virus at 3.3 Å resolution, using single-particle cryo-electron microscopy, together with an atomic model that shows that the N-terminus of the single capsid protein (CP) adopts three different conformations essential for building the interface between geminate halves. Our map also contains density for ~7 bases of single-stranded DNA bound to each CP, and we show that the interactions between the genome and CPs are different at the interface than in the rest of the capsid. With additional mutagenesis data, this suggests a central role for DNA binding-induced conformational change in directing the assembly of geminate capsids.


  • Organizational Affiliation

    Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein195Ageratum yellow vein virusMutation(s): 0 
Gene Names: V1
UniProt
Find proteins for W5RUR4 (Ageratum yellow vein virus)
Explore W5RUR4 
Go to UniProtKB:  W5RUR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5RUR4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
coat protein subunit IQ [auth I]203Ageratum yellow vein virusMutation(s): 0 
Gene Names: V1
UniProt
Find proteins for W5RUR4 (Ageratum yellow vein virus)
Explore W5RUR4 
Go to UniProtKB:  W5RUR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5RUR4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
coat protein subunit HS [auth H]218Ageratum yellow vein virusMutation(s): 0 
Gene Names: V1
UniProt
Find proteins for W5RUR4 (Ageratum yellow vein virus)
Explore W5RUR4 
Go to UniProtKB:  W5RUR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5RUR4
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
ssDNA loop7Ageratum yellow vein virus
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
ssDNA loop associated with subunit HT [auth S]6Ageratum yellow vein virus
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.11
MODEL REFINEMENTREFMAC5

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L021250/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/L020955/1
Wellcome TrustUnited Kingdom108466/Z/15/Z
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J004596/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P012523/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Other