6HKU

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated precision glycooligomers

• PDB DOI: https://doi.org/10.2210/pdb6HKU/pdb

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


• Deposited: 2018-09-08 Released: 2019-03-27 
• Deposition Author(s): Rustmeier, N.H., Stehle, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.230 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

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 Evidence: gel filtration

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: 305.38 kDa 
• Atom Count: 23,268 
• Modelled Residue Count: 2,696 
• Deposited Residue Count: 2,720 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A, B, C, D, E, F, G, H, I, J	272	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-(2-3)-beta-D-galactopyranose	K, L, M	2		N/A
Glycosylation Resources
GlyTouCan:  G30207PZ GlyCosmos:  G30207PZ GlyGen:  G30207PZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	N, O	3		N/A
Glycosylation Resources
GlyTouCan:  G92323ZH GlyCosmos:  G92323ZH GlyGen:  G92323ZH

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA (Subject of Investigation/LOI)	Q [auth D]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N
GOL	P [auth C], R [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900025	N, O	3'-sialyl-alpha-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.230 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.277	α = 90
b = 146.16	β = 90
c = 150.413	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-03-27 
Deposition Author(s): Rustmeier, N.H., Stehle, T.

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Funding Organization	Location	Grant Number
	Germany	FOR2327

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-05-22
  Changes: Data collection, 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: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary