6EK5

Near-atomic resolution structure of a plant geminivirus determined by electron cryo-microscopy.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.6 of the entry. See complete history


Literature

Near-Atomic Resolution Structure of a Plant Geminivirus Determined by Electron Cryomicroscopy.

Hipp, K.Grimm, C.Jeske, H.Bottcher, B.

(2017) Structure 25: 1303-1309.e3

  • DOI: https://doi.org/10.1016/j.str.2017.06.013
  • Primary Citation of Related Structures:  
    6EK5

  • PubMed Abstract: 

    African cassava mosaic virus is a whitefly-transmitted geminivirus which forms unique twin particles of incomplete icosahedra that are joined at five-fold vertices, building an unusual waist. How its 22 capsomers interact within a half-capsid or across the waist is unknown thus far. Using electron cryo-microscopy and image processing, we determined the virion structure with a resolution of 4.2 Å and built an atomic model for its capsid protein. The inter-capsomer contacts mediated by the flexible N termini and loop regions differed within the half-capsids and at the waist, explaining partly the unusual twin structure. The tip of the pentameric capsomer is sealed by a plug formed by a turn region harboring the evolutionary conserved residue Y193. Basic amino acid residues inside the capsid form a positively charged pocket next to the five-fold axis of the capsomer suitable for binding DNA. Within this pocket, density most likely corresponding to DNA was resolved.


  • Organizational Affiliation

    Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart, Germany. Electronic address: katharina.hipp@tuebingen.mpg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein205African cassava mosaic virus - [West Kenya 844]Mutation(s): 0 
Gene Names: AR1AV1
UniProt
Find proteins for P03561 (African cassava mosaic virus (isolate West Kenyan 844))
Explore P03561 
Go to UniProtKB:  P03561
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03561
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references, Other
  • Version 1.2: 2019-11-20
    Changes: Structure summary
  • Version 1.3: 2019-11-27
    Changes: Database references
  • Version 1.4: 2020-02-19
    Changes: Database references
  • Version 1.5: 2020-03-11
    Changes: Database references
  • Version 1.6: 2024-07-10
    Changes: Data collection, Database references