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

Validation slider image for 9AYR

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 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.

Macromolecule Content 

  • Total Structure Weight: 219.34 kDa 
  • Atom Count: 11,962 
  • Modeled Residue Count: 1,501 
  • Deposited Residue Count: 1,934 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  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
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40395
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16664
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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

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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