7PA8 | pdb_00007pa8

JC polyomavirus VP1 in complex with Fab 27C2

• PDB DOI: https://doi.org/10.2210/pdb7PA8/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.213 (DCC) 

Starting Models: experimental

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: Asymmetric - C1 
Global Stoichiometry: Hetero 15-mer - A5B4C3D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 15-mer - A9B5C1 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 479.14 kDa 
• Atom Count: 21,266 
• Modeled Residue Count: 2,846 
• Deposited Residue Count: 4,410 
• Unique protein chains: 3

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]	272	JC polyomavirus	Mutation(s): 0
UniProt
Find proteins for P03089 (JC polyomavirus) Explore P03089  Go to UniProtKB:  P03089

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 27C2 light chain	F [auth FFF], G [auth GGG], I [auth III], K [auth KKK], M [auth MMM]	212	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 27C2 heavy chain	H [auth HHH], J [auth JJJ], L [auth LLL], N [auth NNN], O [auth YYY]	398	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.213 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.07	α = 90
b = 110.44	β = 93.115
c = 158.21	γ = 90

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): Stroeh, L.J., Harprecht, C., 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
• Version 1.2: 2024-10-23
  Changes: Structure summary