8AXJ | pdb_00008axj

Crystal structure of the N-terminal domain of Trypanosoma brucei CFAP410


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 
    0.162 (Depositor), 0.160 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.151 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

CFAP410 has a bimodular architecture with a conserved surface patch on its N-terminal leucine-rich repeat motif for binding interaction partners.

Stadler, A.Gabriel, H.B.De Liz, L.V.Alonso-Gil, S.Deng, X.Crickley, R.Korbula, K.Mikolaskova, B.Vaughan, S.Huang, K.Zagrovic, B.Sunter, J.D.Dong, G.

(2025) Front Cell Dev Biol 13: 1507470-1507470

  • DOI: https://doi.org/10.3389/fcell.2025.1507470
  • Primary Citation of Related Structures:  
    8AXJ

  • PubMed Abstract: 

    Cilia and flagella associated protein 410 (CFAP410) is a protein localized at the basal body of cilia/flagella and plays essential roles in ciliogenesis. Multiple single amino acid mutations in CFAP410 have been identified in patients. However, the molecular mechanism for how the mutations cause these disorders remains poorly understood due to a lack of high-resolution structures of the protein. Our studies demonstrate that CFAP410 adopts a bimodular architecture. We have previously reported our structural studies on the C-terminal domain (CTD) of CFAP410 from various organisms. Here we report a 1.0-Å resolution crystal structure of the N-terminal domain (NTD) of Trypanosoma brucei CFAP410. We further examined how the disease-causing mutations in this domain may affect the folding and structural stability of CFAP410. Our results suggest that the single-residue mutations in the CFAP410-NTD cause human diseases by destabilizing the structure that subsequently disrupts its interaction with other partners.


  • Organizational Affiliation
    • Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chains: A162Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb09.211.3240
UniProt
Find proteins for Q38DI2 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q38DI2 
Go to UniProtKB:  Q38DI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38DI2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free:  0.162 (Depositor), 0.160 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.799α = 90
b = 52.96β = 90
c = 61.433γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaI5960-B2

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection
  • Version 1.2: 2025-03-26
    Changes: Database references, Structure summary