7P5A

Variant Surface Glycoprotein 3 (VSG3, MiTat1.3, VSG224) mutant (serine 317 to alanine), single O-linked glycosylated at Ser319


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Immunodominant surface epitopes power immune evasion in the African trypanosome.

Gkeka, A.Aresta-Branco, F.Triller, G.Vlachou, E.P.van Straaten, M.Lilic, M.Olinares, P.D.B.Perez, K.Chait, B.T.Blatnik, R.Ruppert, T.Verdi, J.P.Stebbins, C.E.Papavasiliou, F.N.

(2023) Cell Rep 42: 112262-112262

  • DOI: https://doi.org/10.1016/j.celrep.2023.112262
  • Primary Citation of Related Structures:  
    7P56, 7P57, 7P59, 7P5A, 7P5B, 7P5D

  • PubMed Abstract: 

    The African trypanosome survives the immune response of its mammalian host by antigenic variation of its major surface antigen (the variant surface glycoprotein or VSG). Here we describe the antibody repertoires elicited by different VSGs. We show that the repertoires are highly restricted and are directed predominantly to distinct epitopes on the surface of the VSGs. They are also highly discriminatory; minor alterations within these exposed epitopes confer antigenically distinct properties to these VSGs and elicit different repertoires. We propose that the patterned and repetitive nature of the VSG coat focuses host immunity to a restricted set of immunodominant epitopes per VSG, eliciting a highly stereotyped response, minimizing cross-reactivity between different VSGs and facilitating prolonged immune evasion through epitope variation.


  • Organizational Affiliation

    Division of Immune Diversity, German Cancer Research Center, 69120 Heidelberg, Germany; Faculty of Biosciences, University of Heidelberg, 69120 Heidelberg, Germany; Panosome GmbH, 69123 Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Variant surface glycoprotein509Trypanosoma brucei bruceiMutation(s): 1 
Gene Names: Tb427.BES153.14Tb427.BES65.13
UniProt
Find proteins for B3GVK1 (Trypanosoma brucei brucei)
Explore B3GVK1 
Go to UniProtKB:  B3GVK1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3GVK1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
6N-Glycosylation
Glycosylation Resources
GlyTouCan:  G56014GC
GlyCosmos:  G56014GC
GlyGen:  G56014GC
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
C [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.396α = 90
b = 129.396β = 90
c = 129.396γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-27
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references
  • Version 2.0: 2023-04-05
    Changes: Atomic model, Data collection, Database references, Source and taxonomy
  • Version 2.1: 2024-02-07
    Changes: Data collection, Refinement description