5LY9 | pdb_00005ly9

Structure of MITat 1.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.205 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5LY9

This is version 2.1 of the entry. See complete history

Literature

Structural basis for the shielding function of the dynamic trypanosome variant surface glycoprotein coat.

Bartossek, T.Jones, N.G.Schafer, C.Cvitkovic, M.Glogger, M.Mott, H.R.Kuper, J.Brennich, M.Carrington, M.Smith, A.S.Fenz, S.Kisker, C.Engstler, M.

(2017) Nat Microbiol 2: 1523-1532

  • DOI: https://doi.org/10.1038/s41564-017-0013-6
  • Primary Citation Related Structures: 
    5LY9, 5M4T

  • PubMed Abstract: 

    The most prominent defence of the unicellular parasite Trypanosoma brucei against the host immune system is a dense coat that comprises a variant surface glycoprotein (VSG). Despite the importance of the VSG family, no complete structure of a VSG has been reported. Making use of high-resolution structures of individual VSG domains, we employed small-angle X-ray scattering to elucidate the first two complete VSG structures. The resulting models imply that the linker regions confer great flexibility between domains, which suggests that VSGs can adopt two main conformations to respond to obstacles and changes of protein density, while maintaining a protective barrier at all times. Single-molecule diffusion measurements of VSG in supported lipid bilayers substantiate this possibility, as two freely diffusing populations could be detected. This translates into a highly flexible overall topology of the surface VSG coat, which displays both lateral movement in the plane of the membrane and variation in the overall thickness of the coat.


  • Organizational Affiliation
    • Department of Cell and Developmental Biology, Theodor-Boveri-Institute, Biocenter, University of Würzburg, 97074, Würzburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 81.85 kDa 
  • Atom Count: 6,649 
  • Modeled Residue Count: 732 
  • Deposited Residue Count: 736 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Variant surface glycoprotein MITAT 1.1
A, B
368Trypanosoma brucei bruceiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P26331 (Trypanosoma brucei brucei)
Explore P26331 
Go to UniProtKB:  P26331
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26331
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
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
C
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G42227JK
GlyCosmos: G42227JK
GlyGen: G42227JK

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.205 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.507α = 90
b = 95.041β = 90
c = 103.753γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyEN 305
German Research FoundationGermanyGRK 1114
German Research FoundationGermanySFB630

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary