Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 159.20 kDa 
• Atom Count: 10211 
• Residue Count: 1294 
• Unique protein chains: 3

6SOZ

Glycosylated Trypanosoma brucei transferrin receptor in complex with human transferrin

• DOI: 10.2210/pdb6SOZ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Trypanosoma brucei, Homo sapiens
• Expression System: Cricetulus longicaudatus, Homo sapiens
• Mutation(s): No 


• Deposited: 2019-08-30 Released: 2019-11-06 
• Deposition Author(s): Trevor, C., Carrington, M., Higgins, M.K.
• Funding Organization(s): Medical Research Council (United Kingdom), Biotechnology and Biological Sciences Research Council, Wellcome Trust, Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.42 Å
• R-Value Free: 0.241 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Literature

Structure of the trypanosome transferrin receptor reveals mechanisms of ligand recognition and immune evasion.

Trevor, C.E., Gonzalez-Munoz, A.L., Macleod, O.J.S., Woodcock, P.G., Rust, S., Vaughan, T.J., Garman, E.F., Minter, R., Carrington, M., Higgins, M.K.

(2019) Nat Microbiol 4: 2074-2081

• PubMed: 31636418 
• DOI: 10.1038/s41564-019-0589-0
• Primary Citation of Related Structures:  
  6SOZ, 6SOY


• PubMed Abstract: 
  

To maintain prolonged infection of mammals, African trypanosomes have evolved remarkable surface coats and a system of antigenic variation ¹ . Within these coats are receptors for macromolecular nutrients such as transferrin ^2,3 . These must be accessible to their ligands but must not confer susceptibility to immunoglobulin-mediated attack. Trypanosomes have a wide host range and their receptors must also bind ligands from diverse species. To understand how these requirements are achieved, in the context of transferrin uptake, we determined the structure of a Trypanosoma brucei transferrin receptor in complex with human transferrin, showing how this heterodimeric receptor presents a large asymmetric ligand-binding platform. The trypanosome genome contains a family of around 14 transferrin receptors ⁴ , which has been proposed to allow binding to transferrin from different mammalian hosts ^5,6 . However, we find that a single receptor can bind transferrin from a broad range of mammals, indicating that receptor variation is unlikely to be necessary for promiscuity of host infection. In contrast, polymorphic sites and N-linked glycans are preferentially found in exposed positions on the receptor surface, not contacting transferrin, suggesting that transferrin receptor diversification is driven by a need for antigenic variation in the receptor to prolong survival in a host.

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Organizational Affiliation: 

Department of Biochemistry, University of Oxford, Oxford, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESAG6, subunit of heterodimeric transferrin receptor	A	399	Trypanosoma brucei	Mutation(s): 0  Gene Names: 13J3.10
Find proteins for Q8WPU1 (Trypanosoma brucei) Explore Q8WPU1  Go to UniProtKB:  Q8WPU1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ESAG7, subunit of heterodimeric transferrin receptor	B	338	Trypanosoma brucei	Mutation(s): 0  Gene Names: 13J3.09
Find proteins for Q8WPU2 (Trypanosoma brucei) Explore Q8WPU2  Go to UniProtKB:  Q8WPU2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Serotransferrin	C	677	Homo sapiens	Mutation(s): 0  Gene Names: TF, PRO1400
Find proteins for P02787 (Homo sapiens) Explore P02787  Go to UniProtKB:  P02787
NIH Common Fund Data Resources
PHAROS:  P02787 GTEx:  ENSG00000091513

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	3		N-Glycosylation

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
FE	C	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.42 Å
• R-Value Free: 0.241 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.18	α = 90
b = 117.87	β = 111.45
c = 134.55	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-08-30 
• Released Date: 2019-11-06 
Deposition Author(s): Trevor, C., Carrington, M., Higgins, M.K.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)		MR/R001138/1
Biotechnology and Biological Sciences Research Council		--
Wellcome Trust		--
Engineering and Physical Sciences Research Council		NS/A000059/1

Revision History 

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary