7PA6

JC polyomavirus VP1 in complex with scFv 27C11

• PDB DOI: https://doi.org/10.2210/pdb7PA6/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, JC polyomavirus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2021-07-29 Released: 2023-02-08 
• Deposition Author(s): Harprecht, C., Stroeh, L.J., Nagel, F., Freytag, J., Stehle, T.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.183 

Literature

Structural characterization of human neutralizing antibodies against JC and BK polyomavirus

Harprecht, C., Stroeh, L.J., Senn, L., O'Hara, B.A., Nagel, F., Freytag, J., Stiehrof, Y.D., Atwood, W.J., Combaluzier, B., Stehle, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A5B5 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A5B5 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 570.5 kDa 
• Atom Count: 40,319 
• Modelled Residue Count: 4,972 
• Deposited Residue Count: 5,250 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv 27C11 antibody heavy chain	A [auth KKK], B [auth LLL], C [auth MMM], D [auth NNN], E [auth OOO], F [auth PPP], G [auth QQQ], H [auth RRR], I [auth SSS], J [auth TTT]	253	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein VP1	K [auth AAA], L [auth BBB], M [auth CCC], N [auth DDD], O [auth EEE], P [auth FFF], Q [auth GGG], R [auth HHH], S [auth III], T [auth JJJ]	272	JC polyomavirus	Mutation(s): 0
UniProt
Find proteins for P03089 (JC polyomavirus) Explore P03089  Go to UniProtKB:  P03089

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.216 
• R-Value Work: 0.183 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.09	α = 100.913
b = 96.11	β = 93.012
c = 190.41	γ = 113.835

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-08 
Deposition Author(s): Harprecht, C., Stroeh, L.J., Nagel, F., Freytag, J., Stehle, T.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FOR2327

Revision History  

• Version 1.0: 2023-02-08
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description