6IAN

T. brucei IFT22/74/81 GTP-bound crystal structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 

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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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intraflagellar transport protein 74A,
C [auth B]
328Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb927.7.3370
UniProt
Find proteins for Q57WF2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q57WF2 
Go to UniProtKB:  Q57WF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57WF2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Intraflagellar transport protein 81B [auth C],
D
454Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb10.70.5020
UniProt
Find proteins for Q38BY1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q38BY1 
Go to UniProtKB:  Q38BY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38BY1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Rab-like 5220Trypanosoma brucei equiperdumMutation(s): 0 
Gene Names: RABL5DPX39_110145000
UniProt
Find proteins for Q381A3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q381A3 
Go to UniProtKB:  Q381A3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ381A3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
F [auth E]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
C [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.86α = 90
b = 228.3β = 96.76
c = 115.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF15OC0014164

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references