4U61

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with 6'-sialyllactose

• PDB DOI: https://doi.org/10.2210/pdb4U61/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Trichodysplasia spinulosa-associated polyomavirus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-26 Released: 2015-08-05 
• Deposition Author(s): Stroh, L.J., Stehle, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.184 
• R-Value Work: 0.165 
• 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)

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 312.64 kDa 
• Atom Count: 23,184 
• Modelled Residue Count: 2,674 
• Deposited Residue Count: 2,800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural protein VP1	A, B, C, D, E, F, G, H, I, J	280	Trichodysplasia spinulosa-associated polyomavirus	Mutation(s): 0  Gene Names: VP1
UniProt
Find proteins for E2ESL7 (Trichodysplasia spinulosa-associated polyomavirus) Explore E2ESL7  Go to UniProtKB:  E2ESL7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose	K	2		N/A
Glycosylation Resources
GlyTouCan:  G63069TR GlyCosmos:  G63069TR GlyGen:  G63069TR

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	L [auth B], N [auth C], O [auth E], S [auth H], T [auth I], U [auth J]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
GOL	M [auth C], P [auth E], Q [auth E], R [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.184 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.56	α = 90
b = 146.35	β = 90
c = 151.54	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Coot	model building
XDS	data reduction
PHASER	phasing
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-05 
Deposition Author(s): Stroh, L.J., Stehle, T.

Revision History  

• Version 1.0: 2015-08-05
  Type: Initial release
  
• Version 1.1: 2015-09-02
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary