Biological Assembly 1  

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 152.14 kDa 
• Atom Count: 11,960 
• Modelled Residue Count: 1,318 
• Deposited Residue Count: 1,350 
• Unique protein chains: 1

 7B6A

BK Polyomavirus VP1 pentamer core (residues 30-299)

• PDB DOI:  https://doi.org/10.2210/pdb7B6A/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Betapolyomavirus hominis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-12-07 Released: 2022-06-22 
• Deposition Author(s): Osipov, E.M., Munawar, A., Beelen, S., Strelkov, S.V.
• Funding Organization(s): Research Foundation - Flanders (FWO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.186 
• R-Value Work: 0.162 

Literature

Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors.

Osipov, E.M., Munawar, A.H., Beelen, S., Fearon, D., Douangamath, A., Wild, C., Weeks, S.D., Van Aerschot, A., von Delft, F., Strelkov, S.V.

(2022) RSC Chem Biol 3: 1013-1027

• PubMed: 35974998 
• DOI: https://doi.org/10.1039/d2cb00052k
• Primary Citation of Related Structures:  
  7B69, 7B6A, 7B6C


• PubMed Abstract: 
  

Polyomaviruses are a family of ubiquitous double-stranded DNA viruses many of which are human pathogens. These include BK polyomavirus which causes severe urinary tract infection in immunocompromised patients and Merkel cell polyomavirus associated with aggressive cancers. The small genome of polyomaviruses lacks conventional drug targets, and no specific drugs are available at present. Here we focus on the main structural protein VP1 of BK polyomavirus which is responsible for icosahedral capsid formation. To provide a foundation towards rational drug design, we crystallized truncated VP1 pentamers and subjected them to a high-throughput screening for binding drug-like fragments through a direct X-ray analysis. To enable a highly performant screening, rigorous optimization of the crystallographic pipeline and processing with the latest generation PanDDA2 software were necessary. As a result, a total of 144 binding hits were established. Importantly, the hits are well clustered in six surface pockets. Three pockets are located on the outside of the pentamer and map on the regions where the 'invading' C-terminal arm of another pentamer is attached upon capsid assembly. Another set of three pockets is situated within the wide pore along the five-fold axis of the VP1 pentamer. These pockets are situated at the interaction interface with the minor capsid protein VP2 which is indispensable for normal functioning of the virus. Here we systematically analyse the three outside pockets which are highly conserved across various polyomaviruses, while point mutations in these pockets are detrimental for viral replication. We show that one of the pockets can accommodate antipsychotic drug trifluoperazine. For each pocket, we derive pharmacophore features which enable the design of small molecules preventing the interaction between VP1 pentamers and therefore inhibiting capsid assembly. Our data lay a foundation towards a rational development of first-in-class drugs targeting polyomavirus capsid.

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Organizational Affiliation: 

Biocrystallography, KU Leuven Herestraat 49 Leuven Belgium [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein VP1	A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD], E [auth EEE]	270	Betapolyomavirus hominis	Mutation(s): 0
UniProt
Find proteins for P03088 (BK polyomavirus) Explore P03088  Go to UniProtKB:  P03088

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	BA [auth CCC], CA [auth CCC], DA [auth CCC], EA [auth CCC], FA [auth CCC], M [auth AAA], MA [auth DDD], N [auth AAA], NA [auth DDD], O [auth AAA], OA [auth DDD], TA [auth EEE], U [auth BBB], UA [auth EEE], V [auth BBB], VA [auth EEE]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
DMS	AA [auth CCC], JA [auth DDD], K [auth AAA], KA [auth DDD], L [auth AAA], LA [auth DDD], RA [auth EEE], S [auth BBB], SA [auth EEE], T [auth BBB], Y [auth CCC], Z [auth CCC]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	F [auth AAA], G [auth AAA], GA [auth DDD], H [auth AAA], HA [auth DDD], I [auth AAA], IA [auth DDD], J [auth AAA], Q [auth BBB], QA [auth EEE], R [auth BBB], W [auth CCC], X [auth CCC]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	P [auth AAA], PA [auth DDD]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 0.186 
• R-Value Work: 0.162 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.622	α = 90
b = 149.719	β = 90
c = 65.488	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-22 
Deposition Author(s): Osipov, E.M., Munawar, A., Beelen, S., Strelkov, S.V.

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Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	G0A5718N

Revision History  

• Version 1.0: 2022-06-22
  Type: Initial release
  
• Version 1.1: 2022-08-31
  Changes: Database references, Derived calculations