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- PDB-9ayr: Structure of a Ric1-Rgp1-Rab6 activation intermediate -

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Basic information

Entry
Database: PDB / ID: 9ayr
TitleStructure of a Ric1-Rgp1-Rab6 activation intermediate
Components
  • GTP-binding protein YPT6
  • Guanine nucleotide exchange factor subunit RGP1
  • Guanine nucleotide exchange factor subunit RIC1
KeywordsPROTEIN TRANSPORT / GEF / GTPASE / RAB
Function / homology
Function and homology information


Ric1-Rgp1 guanyl-nucleotide exchange factor complex / retrograde transport, vesicle recycling within Golgi / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi to endosome transport / cytoplasm to vacuole targeting by the Cvt pathway / guanyl-nucleotide exchange factor complex / protein localization to phagophore assembly site / intra-Golgi vesicle-mediated transport ...Ric1-Rgp1 guanyl-nucleotide exchange factor complex / retrograde transport, vesicle recycling within Golgi / Retrograde transport at the Trans-Golgi-Network / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi to endosome transport / cytoplasm to vacuole targeting by the Cvt pathway / guanyl-nucleotide exchange factor complex / protein localization to phagophore assembly site / intra-Golgi vesicle-mediated transport / cis-Golgi network / protein-containing complex localization / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / phagophore assembly site / retrograde transport, endosome to Golgi / cellular response to nitrogen starvation / Neutrophil degranulation / endomembrane system / guanyl-nucleotide exchange factor activity / macroautophagy / intracellular protein transport / cellular response to heat / Golgi membrane / cell division / GTPase activity / GTP binding / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
Ribosome control protein 1 / Reduced growth phenotype protein 1 / RAB6A-GEF complex partner protein 1 / RIC1 C-terminal alpha solenoid region / Rgp1 / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases ...Ribosome control protein 1 / Reduced growth phenotype protein 1 / RAB6A-GEF complex partner protein 1 / RIC1 C-terminal alpha solenoid region / Rgp1 / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanine nucleotide exchange factor subunit RGP1 / Guanine nucleotide exchange factor subunit RIC1 / GTP-binding protein YPT6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFeathers, J.R. / Fromme, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136258 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for Rab6 activation by the Ric1-Rgp1 complex.
Authors: J Ryan Feathers / Ryan C Vignogna / J Christopher Fromme /
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 ...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.
History
DepositionMar 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
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Revision 1.1Dec 18, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide exchange factor subunit RIC1
B: Guanine nucleotide exchange factor subunit RGP1
C: GTP-binding protein YPT6


Theoretical massNumber of molelcules
Total (without water)219,3453
Polymers219,3453
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Guanine nucleotide exchange factor subunit RIC1 / Protein RIC1 / Ribosome control protein 1 / Ric1p


Mass: 120278.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40395
#2: Protein Guanine nucleotide exchange factor subunit RGP1 / Reduced growth phenotype protein 1 / Rgp1p


Mass: 74621.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P16664
#3: Protein GTP-binding protein YPT6


Mass: 24444.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YPT6, YLR262C, L8479.11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99260
Compound detailsThe authors state that residues were modeled as UNK to denote the uncertainty of a small portion of the model.
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ric1-Rgp1-Ypt6 complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM softwareName: PHENIX / Category: model refinement
Image processing
IDImage recording-ID
11
21
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
13.3FSC 0.143 CUT-OFF6939919AYRPOINT
23.3FSC 0.143 CUT-OFF6939919AYRPOINT
33.3FSC 0.143 CUT-OFF6939929AYRPOINT
43.3FSC 0.143 CUT-OFF6939929AYRPOINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212183
ELECTRON MICROSCOPYf_angle_d0.50416483
ELECTRON MICROSCOPYf_dihedral_angle_d4.0511570
ELECTRON MICROSCOPYf_chiral_restr0.0431934
ELECTRON MICROSCOPYf_plane_restr0.0032057

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