9AYR | pdb_00009ayr

Structure of a Ric1-Rgp1-Rab6 activation intermediate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Resolution: 3.30 Å
  • Resolution: 3.30 Å
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for Rab6 activation by the Ric1-Rgp1 complex.

Feathers, J.R.Vignogna, R.C.Fromme, J.C.

(2024) Nat Commun 15: 10561-10561

  • DOI: https://doi.org/10.1038/s41467-024-54869-9
  • Primary Citation of Related Structures:  
    9AYR

  • PubMed Abstract: 

    Rab GTPases act as molecular switches to regulate organelle homeostasis and membrane trafficking. Rab6 plays a central role in regulating cargo flux through the Golgi and is activated via nucleotide exchange by the Ric1-Rgp1 protein complex. Ric1-Rgp1 is conserved throughout eukaryotes but the structural and mechanistic basis for its function has not been established. Here we report the cryoEM structure of a Ric1-Rgp1-Rab6 complex representing a key intermediate of the nucleotide exchange reaction. Ric1-Rgp1 interacts with the nucleotide-binding domain of Rab6 using an uncharacterized helical domain, which we establish as a RabGEF domain by identifying residues required for Rab6 activation. Unexpectedly, the complex uses an arrestin fold to interact with the Rab6 hypervariable domain, indicating that interactions with the unstructured C-terminal regions of Rab GTPases may be a common binding mechanism used by their activators. Collectively, our findings provide a detailed mechanistic understanding of regulated Rab6 activation at the Golgi.


  • Organizational Affiliation
    • Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14850, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide exchange factor subunit RIC11,056Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P40395 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40395 
Go to UniProtKB:  P40395
Entity Groups  
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UniProt GroupP40395
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide exchange factor subunit RGP1663Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P16664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P16664 
Go to UniProtKB:  P16664
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UniProt GroupP16664
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein YPT6215Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YPT6YLR262CL8479.11
UniProt
Find proteins for Q99260 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q99260 
Go to UniProtKB:  Q99260
Entity Groups  
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UniProt GroupQ99260
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Resolution: 3.30 Å
  • Resolution: 3.30 Å
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM136258

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-11
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-28
    Changes: Data collection