4JCF

S268F Variant of JC Polyomavirus Major Capsid Protein VP1 in Complex with LSTc

• PDB DOI: https://doi.org/10.2210/pdb4JCF/pdb

• Classification: VIRAL PROTEIN
• Organism(s): JC polyomavirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-02-21 Released: 2013-08-14 
• Deposition Author(s): Stehle, T., Stroh, L.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.201 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 151.88 kDa 
• Atom Count: 10,941 
• Modelled Residue Count: 1,287 
• Deposited Residue Count: 1,360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major capsid protein VP1	A [auth C], B [auth A], C [auth B], D, E	272	JC polyomavirus	Mutation(s): 1
UniProt
Find proteins for P03089 (JC polyomavirus) Explore P03089  Go to UniProtKB:  P03089

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N/A
Glycosylation Resources
GlyTouCan:  G73578JC GlyCosmos:  G73578JC GlyGen:  G73578JC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth C], H [auth A], J [auth B], K [auth D], L [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900046	F	6'-sialyl-N-acetyllactosamine	Oligosaccharide / Glycan component

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.201 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.97	α = 90
b = 96.06	β = 110.36
c = 128.22	γ = 90

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Stehle, T., Stroh, L.J.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary