6HKV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


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Literature

Divalent Sialylated Precision Glycooligomers Binding to Polyomaviruses and the Effect of Different Linkers.

Baier, M.Rustmeier, N.H.Harr, J.Cyrus, N.Reiss, G.J.Grafmuller, A.Blaum, B.S.Stehle, T.Hartmann, L.

(2019) Macromol Biosci 19: e1800426-e1800426

  • DOI: 10.1002/mabi.201800426
  • Primary Citation of Related Structures:  
    6HKV, 6HKU

  • PubMed Abstract: 
  • Divalent precision glycooligomers terminating in N-acetylneuraminic acid (Neu5Ac) or 3'-sialyllactose (3'-SL) with varying linkers between scaffold and the glycan portions are synthesized via solid phase synthesis for co-crystallization studies with the sialic acid-binding major capsid protein VP1 of human Trichodysplasia spinulosa-associated Polyomavirus ...

    Divalent precision glycooligomers terminating in N-acetylneuraminic acid (Neu5Ac) or 3'-sialyllactose (3'-SL) with varying linkers between scaffold and the glycan portions are synthesized via solid phase synthesis for co-crystallization studies with the sialic acid-binding major capsid protein VP1 of human Trichodysplasia spinulosa-associated Polyomavirus. High-resolution crystal structures of complexes demonstrate that the compounds bind to VP1 depending on the favorable combination of carbohydrate ligand and linker. It is found that artificial linkers can replace portions of natural carbohydrate linkers as long as they meet certain requirements such as size or flexibility to optimize contact area between ligand and receptor binding sites. The obtained results will influence the design of future high affinity ligands based on the structures presented here, and they can serve as a blueprint to develop multivalent glycooligomers as inhibitors of viral adhesion.


    Organizational Affiliation

    Institute of Organic and Macromolecular Chemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstrasse 1, 40225, Duesseldorf, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid protein VP1
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
272Trichodysplasia spinulosa-associated polyomavirusMutation(s): 0 
Gene Names: VP1
UniProt
Find proteins for E2ESL7 (Trichodysplasia spinulosa-associated polyomavirus)
Explore E2ESL7 
Go to UniProtKB:  E2ESL7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GXB (Subject of Investigation/LOI)
Query on GXB

Download Ideal Coordinates CCD File 
K [auth A] , L [auth B] , M [auth C] , P [auth D] , Q [auth E] , S [auth F] , T [auth G] , V [auth H] , 
K [auth A],  L [auth B],  M [auth C],  P [auth D],  Q [auth E],  S [auth F],  T [auth G],  V [auth H],  W [auth I],  X [auth J]
Sialylated precision glycomacromolecule
C92 H139 N19 O39
NBOMXQZYLQVMQG-PGDFXJOBSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
R [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
O [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
N [auth C], U [auth G]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.4α = 90
b = 145.705β = 90
c = 149.453γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
GermanyFOR2327

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references