2YC2 | pdb_00002yc2

Intraflagellar Transport Complex 25-27 from Chlamydomonas


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.266 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Intraflagellar Transport Complex 25/27.

Bhogaraju, S.Taschner, M.Morawetz, M.Basquin, C.Lorentzen, E.

(2011) EMBO J 30: 1907

  • DOI: https://doi.org/10.1038/emboj.2011.110
  • Primary Citation Related Structures: 
    2YC2, 2YC4

  • PubMed Abstract: 

    The cilium is an important organelle that is found on many eukaryotic cells, where it serves essential functions in motility, sensory reception and signalling. Intraflagellar transport (IFT) is a vital process for the formation and maintenance of cilia. We have determined the crystal structure of Chlamydomonas reinhardtii IFT25/27, an IFT sub-complex, at 2.6 Å resolution. IFT25 and IFT27 interact via a conserved interface that we verify biochemically using structure-guided mutagenesis. IFT27 displays the fold of Rab-like small guanosine triphosphate hydrolases (GTPases), binds GTP and GDP with micromolar affinity and has very low intrinsic GTPase activity, suggesting that it likely requires a GTPase-activating protein (GAP) for robust GTP turnover. A patch of conserved surface residues contributed by both IFT25 and IFT27 is found adjacent to the GTP-binding site and could mediate the binding to other IFT proteins as well as to a potential GAP. These results provide the first step towards a high-resolution structural understanding of the IFT complex.


  • Organizational Affiliation
    • Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 77.6 kDa 
  • Atom Count: 4,339 
  • Modeled Residue Count: 561 
  • Deposited Residue Count: 694 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INTRAFLAGELLAR TRANSPORT PROTEIN 25
A, B
139Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for B8LIX8 (Chlamydomonas reinhardtii)
Explore B8LIX8 
Go to UniProtKB:  B8LIX8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8LIX8
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SMALL RAB-RELATED GTPASE
C, D
208Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8HN58 (Chlamydomonas reinhardtii)
Explore A8HN58 
Go to UniProtKB:  A8HN58
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HN58
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.266 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.05α = 90
b = 96.22β = 89.97
c = 66.97γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-05-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description