4P17

Crystal structure of the Chlamydomonas flagellar RabGAP TBC domain.

• PDB DOI: https://doi.org/10.2210/pdb4P17/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2014-02-25 Released: 2014-04-30 
• Deposition Author(s): Bhogaraju, S., Lorentzen, E.
• Funding Organization(s): European Research Council (ERC), Emmy Noether grant

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.260 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Crystal structure of a Chlamydomonas reinhardtii flagellar RabGAP TBC-domain at 1.8 angstrom resolution.

Bhogaraju, S., Lorentzen, E.

(2014) Proteins 82: 2282-2287

• PubMed: 24810373 
• DOI: https://doi.org/10.1002/prot.24597
• Primary Citation of Related Structures:  
  4P17


• PubMed Abstract: 
  

  Rab GTPases play a crucial role in the regulation of many intracellular membrane trafficking pathways including endocytosis and ciliogenesis. Rab GTPase activating proteins (RabGAPs) increase the GTP hydrolysis rate of Rab GTPases and turn them into guanine nucleotide diphosphate (GDP) bound inactive form. Here, we determined the crystal structure of the putative catalytic domain of a RabGAP (which we name CrfRabGAP) that is found in the flagellar proteome of the unicellular green alga Chlamydomonas reinhardtii. BLAST searches revealed potential human orthologues of CrfRabGAP as TBC1D3 and TBC1D26. Sequence and structural comparison with other canonical RabGAPs revealed that the CrfRabGAP does not contain the canonical catalytic residues required for the activation of Rab GTPases. The function of noncanonical RabGAPs-like CrfRabGAP might be to serve as Rab effectors rather than activators.

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Organizational Affiliation: 

Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.35 kDa 
• Atom Count: 5,334 
• Modelled Residue Count: 578 
• Deposited Residue Count: 626 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RabGAP/TBC protein	A, B	313	Chlamydomonas reinhardtii	Mutation(s): 0  Gene Names: CHLREDRAFT_195581

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 0.260 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.76	α = 90
b = 47.01	β = 96.33
c = 105.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Bhogaraju, S., Lorentzen, E.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	310343
Emmy Noether grant	Germany	DGF; LO1627/1-1

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Database references
• Version 1.2: 2014-10-01
  Changes: Database references
• Version 1.3: 2017-09-27
  Changes: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.4: 2020-01-08
  Changes: Author supporting evidence
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Refinement description