7ZIP | pdb_00007zip

JC Polyomavirus VP1 in complex with 3'-Sialyllactose glycomacromolecules (aliphatic linker)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.215 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.181 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Synthesis of Homo- and Heteromultivalent Fucosylated and Sialylated Oligosaccharide Conjugates via Preactivated N -Methyloxyamine Precision Macromolecules and Their Binding to Polyomavirus Capsid Proteins.

Konietzny, P.B.Freytag, J.Feldhof, M.I.Muller, J.C.Ohl, D.Stehle, T.Hartmann, L.

(2022) Biomacromolecules 23: 5273-5284

  • DOI: https://doi.org/10.1021/acs.biomac.2c01092
  • Primary Citation Related Structures: 
    7ZIL, 7ZIM, 7ZIN, 7ZIO, 7ZIP, 7ZIQ

  • PubMed Abstract: 

    Glycoconjugates are a versatile class of bioactive molecules that have found application as vaccines and antivirals and in cancer therapy. Their synthesis typically involves elaborate functionalization and use of protecting groups on the carbohydrate component in order to ensure efficient and selective conjugation. Alternatively, non-functionalized, non-protected carbohydrates isolated from biological sources or derived through biotechnological methods can be directly conjugated via N -methyloxyamine groups. In this study, we introduce such N -methyloxyamine groups into a variety of multivalent scaffolds─from small to oligomeric to polymeric scaffolds─making use of solid-phase polymer synthesis to assemble monodisperse sequence-defined macromolecules. These scaffolds are then successfully functionalized with different types of human milk oligosaccharides deriving a library of homo- and heteromultivalent glycoconjugates. Glycomacromolecules presenting oligosaccharide side chains with either α2,3- or α2,6-linked terminal sialic acid are used in a binding study with two types of polyomavirus capsid proteins showing that the multivalent presentation through the N -methyloxyamine-derived scaffolds increases the number of contacts with the protein. Overall, a straightforward route to derive glycoconjugates from complex oligosaccharides with high variability yet control in the multivalent scaffold is presented, and applicability of the derived structures is demonstrated.


  • Organizational Affiliation
    • Department of Organic and Macromolecular Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany.

Macromolecule Content 

  • Total Structure Weight: 151.94 kDa 
  • Atom Count: 10,755 
  • Modeled Residue Count: 1,287 
  • Deposited Residue Count: 1,375 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Major capsid protein VP1A [auth AAA],
B [auth BBB],
C [auth CCC],
D [auth DDD],
E [auth EEE]
275Betapolyomavirus hominisMutation(s): 3 
UniProt
Find proteins for P03088 (BK polyomavirus)
Explore P03088 
Go to UniProtKB:  P03088
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03088
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseF [auth DaD]3N/A
Glycosylation Resources
GlyTouCan: G91237TK
GlyCosmos: G91237TK
GlyGen: G91237TK

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.215 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.181 (DCC) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.734α = 90
b = 152.505β = 90
c = 62.952γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyFOR2327

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-21
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description