6Z7A | pdb_00006z7a

Variant Surface Glycoprotein VSGsur

• PDB DOI: https://doi.org/10.2210/pdb6Z7A/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Trypanosoma brucei rhodesiense
• Expression System: Trypanosoma brucei brucei
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2020-05-30 Released: 2021-05-26 
• Deposition Author(s): Zeelen, J.P., Straaten van, M., Stebbins, C.E., Hashemi, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free: 
  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

A Parasite Coat Protein Binds Suramin to Confer Drug Resistance

Zeelen, J.P., van Straaten, M., Verdi, J., Hempelmann, A., Hashemi, H., Perez, K., Jeffrey, P.D., Haelg, S., Wiedemar, N., Maeser, P., Papavasiliou, F.N., Stebbins, C.E.

(2021) Nat Microbiol 6: 392-400

• DOI: https://doi.org/10.1038/s41564-020-00844-1

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.54 kDa 
• Atom Count: 3,142 
• Modeled Residue Count: 359 
• Deposited Residue Count: 491 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Variant surface glycoprotein Sur	A	491	Trypanosoma brucei rhodesiense	Mutation(s): 0  Gene Names: VSGsur Membrane Entity: Yes
UniProt
Find proteins for A0A291L8F4 (Trypanosoma brucei rhodesiense) Explore A0A291L8F4  Go to UniProtKB:  A0A291L8F4
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.21 Å
• R-Value Free:  0.187 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.042	α = 90
b = 71.062	β = 90
c = 130.453	γ = 90

Software Package:

Software Name	Purpose
AutoProcess	data collection
PHENIX	refinement
Coot	model building
pointless	data scaling
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-26 
Deposition Author(s): Zeelen, J.P., Straaten van, M., Stebbins, C.E., Hashemi, H.

Revision History  

• Version 1.0: 2021-05-26
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary