7PA9 | pdb_00007pa9

JC polyomavirus VP1 in complex with Fab 98D3

• PDB DOI: https://doi.org/10.2210/pdb7PA9/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: 2.75 Å
• R-Value Free: 
  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (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 - A5B5C4D1 Pseudo Symmetry: Cyclic - C5  (Explore in 3D)
Pseudo Stoichiometry: Hetero 15-mer - A10B5 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Hetero 10-mer - A5B5 

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Hetero 15-mer - A5B5C5 Pseudo Symmetry: Cyclic - C5  (Explore in 3D)
Pseudo Stoichiometry: Hetero 15-mer - A10B5 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 971.33 kDa 
• Atom Count: 51,021 
• Modeled Residue Count: 6,672 
• Deposited Residue Count: 8,880 
• 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], F [auth FFF], G [auth GGG], H [auth HHH], I [auth III], J [auth JJJ]	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 98D3 VH	BA [auth bbb], CA [auth ccc], K [auth KKK], M [auth MMM], O [auth OOO], Q [auth QQQ], T [auth TTT], V [auth VVV], X [auth XXX], Y [auth YYY]	404	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 98D3 VL	AA [auth aaa], DA [auth ddd], L [auth LLL], N [auth NNN], P [auth PPP], R [auth RRR], S [auth SSS], U [auth UUU], W [auth WWW], Z [auth ZZZ]	212	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.263 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.97	α = 90
b = 202.31	β = 90
c = 251.66	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