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 7PA7 | pdb_00007pa7

BK polyomavirus VP1 in complex with scFv 29B1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.272 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.247 (Depositor), 0.249 (DCC) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7PA7

This is version 1.3 of the entry. See complete history. 

Literature

Structural characterization of human neutralizing antibodies against JC and BK polyomaviruses.

Harprecht, C., Stroh, L.J., O'Hara, B.A., Freytag, J., Nagel, F., Haley, S.A., Stierhof, Y.D., Atwood, W.J., Stehle, T.

(2026) Proc Natl Acad Sci U S A 123: e2603048123-e2603048123

  • DOI: https://doi.org/10.1073/pnas.2603048123
  • Primary Citation Related Structures: 
    7PA6, 7PA7, 7PA8, 7PA9, 7PAA

  • PubMed Abstract: 

    The human JC polyomavirus (JCPyV) causes the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML) in immunocompromised individuals. JCPyV frequently undergoes mutations in PML patients, and these variants are thought to establish "antibody recognition holes" that enable the virus to circumvent the antibody response of infected individuals. Many of these PML-associated mutations cluster in the glycan receptor-binding site of the virus. Using X-ray crystallography, we investigated the binding modes of JCPyV VP1-specific human monoclonal antibodies (mAbs) that were isolated from healthy donors and individuals who recovered from PML, and that can recognize a panel of PML-associated JCPyV variants. Our structural analyses show that three out of four of these mAbs bind epitopes that overlap with the glycan-receptor binding site at the surface of the virus particle. The observed interactions explain how PML-associated mutations strategically interfere with antibody recognition, resulting in immune evasion. In contrast, mAb 29B1 engages a region of the capsid that is distant from the glycan site and does not feature mutations associated with PML. The binding site is conserved in the closely related BK polyomavirus (BKPyV), and we show that mAb 29B1 binds both viruses with high affinity and blocks infection. Our findings form an excellent platform for the development of therapeutic Ab approaches and potential vaccination strategies that could protect at-risk patients from infections with both JCPyV and BKPyV. Moreover, small molecules that target the mAb 29B1 binding site could be potentially effective against both viruses.


  • Organizational Affiliation: 
    • Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 572.09 kDa 
  • Atom Count: 37,703 
  • Modeled Residue Count: 4,867 
  • Deposited Residue Count: 5,270 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
scFv 29B1 antibody heavy chain252Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Major capsid protein VP1275Betapolyomavirus hominisMutation(s): 3 
UniProt
Find proteins for P03088 (BK polyomavirus)
Explore P03088 
Go to UniProtKB:  P03088
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03088
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.272 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.247 (Depositor), 0.249 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.588α = 92.315
b = 114.614β = 105.996
c = 142.373γ = 111.407
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFOR2327

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-20
    Changes: Structure summary
  • Version 1.3: 2026-10-21
    Changes: Database references