6GG0

Cryo-EM structure of BK polyomavirus like particle in complex with single chain antibody ScFv41F17


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.24 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

Human Memory B Cells Harbor Diverse Cross-Neutralizing Antibodies against BK and JC Polyomaviruses.

Lindner, J.M.Cornacchione, V.Sathe, A.Be, C.Srinivas, H.Riquet, E.Leber, X.C.Hein, A.Wrobel, M.B.Scharenberg, M.Pietzonka, T.Wiesmann, C.Abend, J.Traggiai, E.

(2019) Immunity 50: 668-676.e5

  • DOI: 10.1016/j.immuni.2019.02.003
  • Primary Citation of Related Structures:  
    6GG0

  • PubMed Abstract: 
  • Human polyomaviruses cause a common childhood infection worldwide and typically elicit a neutralizing antibody and cellular immune response, while establishing a dormant infection in the kidney with minimal clinical manifestations. However, viral reactivation can cause severe pathology in immunocompromised individuals ...

    Human polyomaviruses cause a common childhood infection worldwide and typically elicit a neutralizing antibody and cellular immune response, while establishing a dormant infection in the kidney with minimal clinical manifestations. However, viral reactivation can cause severe pathology in immunocompromised individuals. We developed a high-throughput, functional antibody screen to examine the humoral response to BK polyomavirus. This approach enabled the isolation of antibodies from all peripheral B cell subsets and revealed the anti-BK virus antibody repertoire as clonally complex with respect to immunoglobulin sequences and isotypes (both IgM and IgG), including a high frequency of monoclonal antibodies that broadly neutralize BK virus subtypes and the related JC polyomavirus. Cryo-electron microscopy of a broadly neutralizing IgG single-chain variable fragment complexed with BK virus-like particles revealed the quaternary nature of a conserved viral epitope at the junction between capsid pentamers. These features unravel a potent modality for inhibiting polyomavirus infection in kidney transplant recipients and other immunocompromised patients.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Basel, Switzerland, Cambridge, MA, USA, and Emeryville, CA, USA. Electronic address: elisabetta.traggiai@novartis.com.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP1A [auth 1], B [auth 2], C [auth 3], D [auth 4], E [auth 5], F [auth 6]362Human polyomavirus 1Mutation(s): 0 
Gene Names: VP1BK1035_00004BK1055_00004
Find proteins for P03088 (BK polyomavirus)
Explore P03088 
Go to UniProtKB:  P03088
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy chainG [auth H]124Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
light chainH [auth L]109Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2018-05-02 
  • Released Date: 2019-03-06 
  • Deposition Author(s): Srinivas, H.

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-11
    Changes: Other