6IA7

T. brucei IFT22 GTP-bound crystal structure

• PDB DOI: https://doi.org/10.2210/pdb6IA7/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-26 Released: 2019-04-10 
• Deposition Author(s): Wachter, S., Basquin, J., Lorentzen, E.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.264 
• R-Value Work: 0.212 
• R-Value Observed: 0.217 

Literature

Binding of IFT22 to the intraflagellar transport complex is essential for flagellum assembly.

Wachter, S., Jung, J., Shafiq, S., Basquin, J., Fort, C., Bastin, P., Lorentzen, E.

(2019) EMBO J 38

• PubMed: 30940671 
• DOI: https://doi.org/10.15252/embj.2018101251
• Primary Citation of Related Structures:  
  6IA7, 6IAE, 6IAN


• PubMed Abstract: 
  

  Intraflagellar transport (IFT) relies on motor proteins and the IFT complex to construct cilia and flagella. The IFT complex subunit IFT22/RabL5 has sequence similarity with small GTPases although the nucleotide specificity is unclear because of non-conserved G4/G5 motifs. We show that IFT22 specifically associates with G-nucleotides and present crystal structures of IFT22 in complex with GDP, GTP, and with IFT74/81. Our structural analysis unravels an unusual GTP/GDP-binding mode of IFT22 bypassing the classical G4 motif. The GTPase switch regions of IFT22 become ordered upon complex formation with IFT74/81 and mediate most of the IFT22-74/81 interactions. Structure-based mutagenesis reveals that association of IFT22 with the IFT complex is essential for flagellum construction in Trypanosoma brucei although IFT22 GTP-loading is not strictly required.

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Organizational Affiliation: 

Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 50.7 kDa 
• Atom Count: 2,336 
• Modelled Residue Count: 298 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intraflagellar transport protein 22	A, B	223	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: IFT22, Tb11.01.8590
UniProt
Find proteins for Q381A3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q381A3  Go to UniProtKB:  Q381A3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	C [auth A], F [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.264 
• R-Value Work: 0.212 
• R-Value Observed: 0.217 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.845	α = 90
b = 55.845	β = 90
c = 263.443	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Wachter, S., Basquin, J., Lorentzen, E.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF15OC0014164

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Database references