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- EMDB-43997: Structure of a Ric1-Rgp1-Rab6 activation intermediate -

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Basic information

Entry
Database: EMDB / ID: EMD-43997
TitleStructure of a Ric1-Rgp1-Rab6 activation intermediate
Map dataRefinement full map
Sample
  • Complex: Ric1-Rgp1-Ypt6 complex
    • Protein or peptide: Guanine nucleotide exchange factor subunit RIC1
    • Protein or peptide: Guanine nucleotide exchange factor subunit RGP1
    • Protein or peptide: GTP-binding protein YPT6
KeywordsGEF / GTPASE / RAB / PROTEIN TRANSPORT
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 / intracellular protein transport / macroautophagy / 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 Rab1 family 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 Rab1 family 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) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFeathers JR / Fromme JC
Funding support United States, 1 items
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, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43997.png

Downloads & links

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Map

FileDownload / File: emd_43997.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefinement full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 196 pix.
= 245. Å		1.25 Å/pix.
x 196 pix.
= 245. Å		1.25 Å/pix.
x 196 pix.
= 245. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.049608495 - 0.11779761
Average (Standard dev.)0.0000281936 (±0.0038821567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 245.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local resolution sharpened map

Fileemd_43997_additional_1.map
AnnotationLocal resolution sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from masked refinement

Fileemd_43997_half_map_1.map
AnnotationHalf map 2 from masked refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from masked refinement

Fileemd_43997_half_map_2.map
AnnotationHalf map 1 from masked refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ric1-Rgp1-Ypt6 complex

EntireName: Ric1-Rgp1-Ypt6 complex
Components
  • Complex: Ric1-Rgp1-Ypt6 complex
    • Protein or peptide: Guanine nucleotide exchange factor subunit RIC1
    • Protein or peptide: Guanine nucleotide exchange factor subunit RGP1
    • Protein or peptide: GTP-binding protein YPT6

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Supramolecule #1: Ric1-Rgp1-Ypt6 complex

SupramoleculeName: Ric1-Rgp1-Ypt6 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Guanine nucleotide exchange factor subunit RIC1

MacromoleculeName: Guanine nucleotide exchange factor subunit RIC1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 120.27882 KDa
SequenceString: MFIKQSEKNT PKCLYKKKGK VRVLLTGSCK KLNTWKMHLW PVSPPQLLRI PPRNAELGEG TKIDDCNILQ SMTLPQANVL IMLTPTRVL IYNFKPMALV ASHERTMASL KEFGDNRSMK RSAPYNDIIE GLISKKDSQY LLWHQGKLIF YVMTDKNFLL T YQILKNCT ...String:
MFIKQSEKNT PKCLYKKKGK VRVLLTGSCK KLNTWKMHLW PVSPPQLLRI PPRNAELGEG TKIDDCNILQ SMTLPQANVL IMLTPTRVL IYNFKPMALV ASHERTMASL KEFGDNRSMK RSAPYNDIIE GLISKKDSQY LLWHQGKLIF YVMTDKNFLL T YQILKNCT NEIIFKEYGI PVIEPLLMSE EEANSAEYDY NNDDDTLTVF DKNSSSRIIQ NGFGITKEKG FLHFLSNQEN ID ELPVKKL ELRLKVVLKF DYEIIDMIGI KTFSKVGDGR YEEVLIVLFP HGLQILTISD FKVSKSSLVE VKKGSKTIVC NKQ LMVLSH DSVEKQTIVS IIDIEKQAVE AIPLTDTPDE LLTCLEVNGY LVVVYKEKII CFDTRIKKVS HSWKPPFVIK LCDK INDKI LLLVSEDSVN IHFYTEFGNL LFATYFDEDD YNGDNNNDNS KDKNEKKAAE YKISDFVCLD KSLITVSHSG KYQVW KLWE EIKQTQFDFR NPKCYVLTNT NNDVIIYSPV TSSSINNDNL QVIKLPTKTF NNHIAFVKIN SSLRLFATYV SNKNIL LIH NLETNMWSSF ADQNVLDLHW LGDNYLVCHM KNDDGSTNLK CLQIPLQEAN PDVELSDYVM WEYNVPENTI VFSLHVN TL SRYKLLKMKS KNHNASEKQP DALLKTAEII LVTDTQTIVF DVISTVHPCG LNIIKKFYQY LKINIPIDVL PNKIEWII N MKEGLLFFAD RKFIKLGKVD GGGWQTLTLL DNIEKIIDVI RDEIFVVQGH NYVVYSLEDL WDDKKPLVSI PIEEDLYPI STTPETATTH TLHCIFNARF SKLVVKHQIY LDQLILAKLE DNTDLEDISH NYRFLKPYKF ALEKILSTKI LRSDSLDDIL KLIKMYDNT DPEHNISPPT HSGMLEIISN CLRKIETKYW NHLFTNLKMT PRDLLALCIE ENEAKMLGVL LLVFLNYDEK D LGDDLHFK KSDLGTEESK ALNDNSTKKS EKSVTNLLK(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)AT D(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) DRENNT Q(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

UniProtKB: Guanine nucleotide exchange factor subunit RIC1

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Macromolecule #2: Guanine nucleotide exchange factor subunit RGP1

MacromoleculeName: Guanine nucleotide exchange factor subunit RGP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 74.621453 KDa
SequenceString: MRAHRIDTFL IRENIKLEII HESNSYFGGE HISIAFRFKH LGSQHELFNY KEKLLTVDKA VEEKLEQQAK VQDDGEGTME NQTWSLKSL LGAFKRTGEP EESVDVDNMK MLNESKMLRE KIQKQMYFHQ PVTLISGYVQ ISGVFQYDSE VISESKFKQD E VKMVGLDI ...String:
MRAHRIDTFL IRENIKLEII HESNSYFGGE HISIAFRFKH LGSQHELFNY KEKLLTVDKA VEEKLEQQAK VQDDGEGTME NQTWSLKSL LGAFKRTGEP EESVDVDNMK MLNESKMLRE KIQKQMYFHQ PVTLISGYVQ ISGVFQYDSE VISESKFKQD E VKMVGLDI VPGHTTNSVL ALEDGEHFKG KRNLTNYLNS DYTNVTNGLL FSESGSRGRT GTYNERTLMI SNDTSIKTLP LL LIPQTLL FSEISLEPGE VRTFYFKSTK LPKDICPSYS SSKVASINYT LEVGADVLSD DNIEKFSNRV PITIAPYISS NAE QYTSRL DKPAIILKTG NIKELKPRLF TRKVSTASAV SFGRRKSSII DIDSPLEDNE FV(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)SNQNV SR(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)QFGKD EDSSDPEPND SHFSNEMVTS AESSLRSDAV TKRRKSYSVR DNISN LEQK MWNDCSLVKS DENSNLLPQL INLQNAYQIN RNNETMAKVS LSAPFYKTTD DINLVIELDP ITTPLLKVTS LTVSLE SFE IINPKYKTEG KGIGSKPKGN SVYEKHFICF DECKSVSVKL LPPRSPTNQI TGQFKTDVFQ HKWMIGLKFV IIAKTES IT LDQFYEDKKG ILFHSKENLE GEEFTCYVPI PILCTSEDFM GW

UniProtKB: Guanine nucleotide exchange factor subunit RGP1

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Macromolecule #3: GTP-binding protein YPT6

MacromoleculeName: GTP-binding protein YPT6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.444609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSRSGKSLTK YKIVFLGEQG VGKTSLITRF MYDTFDDHYQ ATIGIDFLSK TMYLDDKTIR LQLWDTAGQE RFRSLIPSYI RDSRVAIIV YDITKRKSFE YIDKWIEDVK NERGDENVIL CIVGNKSDLS DERQISTEEG EKKAKLLGAK IFMETSTKAG Y NVKALFKK ...String:
MSRSGKSLTK YKIVFLGEQG VGKTSLITRF MYDTFDDHYQ ATIGIDFLSK TMYLDDKTIR LQLWDTAGQE RFRSLIPSYI RDSRVAIIV YDITKRKSFE YIDKWIEDVK NERGDENVIL CIVGNKSDLS DERQISTEEG EKKAKLLGAK IFMETSTKAG Y NVKALFKK IAKSLPEFQN SESTPLDSEN ANSANQNKPG VIDISTAEEQ EQSACQC

UniProtKB: GTP-binding protein YPT6

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AB INITIO
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69399
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AB INITIO
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69399
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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