Variant Surface Glycoprotein VSG615

Experimental Data Snapshot

  • Resolution: 3.22 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.307 
  • R-Value Observed: 0.308 

Starting Model: in silico
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Ligand Structure Quality Assessment 

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A structural classification of the variant surface glycoproteins of the African trypanosomey.

Dakovic, S.Zeelen, J.P.Gkeka, A.Chandra, M.van Straaten, M.Foti, K.Zhong, J.Vlachou, E.P.Aresta-Branco, F.Verdi, J.P.Papavasiliou, F.N.Stebbins, C.E.

(2023) PLoS Negl Trop Dis 17: e0011621-e0011621

  • DOI: https://doi.org/10.1371/journal.pntd.0011621
  • Primary Citation of Related Structures:  
    8OK4, 8OK5, 8OK6, 8OK7, 8OK8, 8ONH, 8Q0E, 8Q0P

  • PubMed Abstract: 

    Long-term immune evasion by the African trypanosome is achieved through repetitive cycles of surface protein replacement with antigenically distinct versions of the dense Variant Surface Glycoprotein (VSG) coat. Thousands of VSG genes and pseudo-genes exist in the parasite genome that, together with genetic recombination mechanisms, allow for essentially unlimited immune escape from the adaptive immune system of the host. The diversity space of the "VSGnome" at the protein level was thought to be limited to a few related folds whose structures were determined more than 30 years ago. However, recent progress has shown that the VSGs possess significantly more architectural variation than had been appreciated. Here we combine experimental X-ray crystallography (presenting structures of N-terminal domains of coat proteins VSG11, VSG21, VSG545, VSG558, and VSG615) with deep-learning prediction using Alphafold to produce models of hundreds of VSG proteins. We classify the VSGnome into groups based on protein architecture and oligomerization state, contextualize recent bioinformatics clustering schemes, and extensively map VSG-diversity space. We demonstrate that in addition to the structural variability and post-translational modifications observed thus far, VSGs are also characterized by variations in oligomerization state and possess inherent flexibility and alternative conformations, lending additional variability to what is exposed to the immune system. Finally, these additional experimental structures and the hundreds of Alphafold predictions confirm that the molecular surfaces of the VSGs remain distinct from variant to variant, supporting the hypothesis that protein surface diversity is central to the process of antigenic variation used by this organism during infection.

  • Organizational Affiliation

    Division of Structural Biology of Infection and Immunity, German Cancer Research Center, Heidelberg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Variant surface glycoprotein 615376Trypanosoma brucei bruceiMutation(s): 0 
Find proteins for M4SXH7 (Trypanosoma brucei)
Explore M4SXH7 
Go to UniProtKB:  M4SXH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM4SXH7
Glycosylation Sites: 1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth J],
H [auth F]
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth C],
O [auth G],
T [auth K]
C8 H15 N O6
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
K [auth C]
L [auth C]
M [auth E]
N [auth E]
P [auth G]
K [auth C],
L [auth C],
M [auth E],
N [auth E],
P [auth G],
Q [auth G],
R [auth I],
S [auth I],
U [auth K],
V [auth K]
C6 H12 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 3.22 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.307 
  • R-Value Observed: 0.308 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.28α = 90
b = 111.23β = 91.65
c = 108.59γ = 90
Software Package:
Software NamePurpose
Cootmodel building
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release