8B3E | pdb_00008b3e

Variant Surface Glycoprotein VSG397


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 
    0.216 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8B3E

This is version 1.2 of the entry. See complete history

Literature

Structural similarities between the metacyclic and bloodstream form variant surface glycoproteins of the African trypanosome.

Chandra, M.Dakovic, S.Foti, K.Zeelen, J.P.van Straaten, M.Aresta-Branco, F.Tihon, E.Lubbehusen, N.Ruppert, T.Glover, L.Papavasiliou, F.N.Stebbins, C.E.

(2023) PLoS Negl Trop Dis 17: e0011093-e0011093

  • DOI: https://doi.org/10.1371/journal.pntd.0011093
  • Primary Citation Related Structures: 
    8B3B, 8B3E, 8B3W

  • PubMed Abstract: 

    During infection of mammalian hosts, African trypanosomes thwart immunity using antigenic variation of the dense Variant Surface Glycoprotein (VSG) coat, accessing a large repertoire of several thousand genes and pseudogenes, and switching to antigenically distinct copies. The parasite is transferred to mammalian hosts by the tsetse fly. In the salivary glands of the fly, the pathogen adopts the metacyclic form and expresses a limited repertoire of VSG genes specific to that developmental stage. It has remained unknown whether the metacyclic VSGs possess distinct properties associated with this particular and discrete phase of the parasite life cycle. We present here three novel metacyclic form VSG N-terminal domain crystal structures (mVSG397, mVSG531, and mVSG1954) and show that they mirror closely in architecture, oligomerization, and surface diversity the known classes of bloodstream form VSGs. These data suggest that the mVSGs are unlikely to be a specialized subclass of VSG proteins, and thus could be poor candidates as the major components of prophylactic vaccines against trypanosomiasis.


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

Macromolecule Content 

  • Total Structure Weight: 45.88 kDa 
  • Atom Count: 3,366 
  • Modeled Residue Count: 389 
  • Deposited Residue Count: 437 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Variant surface glycoprotein 397437Trypanosoma bruceiMutation(s): 0 
UniProt
Find proteins for M4SY06 (Trypanosoma brucei)
Explore M4SY06 
Go to UniProtKB:  M4SY06
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupM4SY06
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.557α = 90
b = 218.484β = 90
c = 66.436γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
BUCCANEERmodel building
XDSdata reduction
Aimlessdata scaling
SHELXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Data collection, Structure summary