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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This is version 1.1 of the entry. See complete history


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: 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 ...

    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 Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark el@mbg.au.dk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Rab-like 5E220Trypanosoma 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / 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
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth E]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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