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- EMDB-54212: Ypt7 in complex with its GEF Mon1-Ccz1 -

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Basic information

Entry
Database: EMDB / ID: EMD-54212
TitleYpt7 in complex with its GEF Mon1-Ccz1
Map data
Sample
  • Complex: Complex of nucleotide free Ypt7 with its GEF Mon1-Ccz1
    • Protein or peptide: Rab small monomeric GTPase-like protein
    • Protein or peptide: Vacuolar fusion protein MON1
    • Protein or peptide: CCZ1/INTU/HSP4 first Longin domain-containing protein
Keywordslongin domain / GEF / nucleotide exchange / endosome / autophagosome / small GTPase / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


Mon1-Ccz1 complex / regulation of vacuole fusion, non-autophagic / protein targeting to vacuole / multivesicular body membrane / fungal-type vacuole membrane / vesicle-mediated transport / autophagy / late endosome / GTPase activity / GTP binding
Similarity search - Function
Vacuolar fusion protein Ccz1 / Vacuolar fusion protein Mon1 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 / Second Longin domain of FUZ, MON1 and HPS1 / Third Longin domain of FUZ, MON1 and HPS1 ...Vacuolar fusion protein Ccz1 / Vacuolar fusion protein Mon1 / CCZ1/INTU/HSP4, first Longin domain / First Longin domain of INTU, CCZ1 and HPS4 / FUZ/MON1/HPS1, third Longin domain / FUZ/MON1/HPS1, second Longin domain / FUZ/MON1/HPS1, first Longin domain / First Longin domain of FUZ, MON1 and HPS1 / Second Longin domain of FUZ, MON1 and HPS1 / Third Longin domain of FUZ, MON1 and HPS1 / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase Ras 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
CCZ1/INTU/HSP4 first Longin domain-containing protein / Rab small monomeric GTPase-like protein / Vacuolar fusion protein MON1
Similarity search - Component
Biological speciesThermochaetoides thermophila (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWilmes S / Schaefer J / Moeller A / Kuemmel D
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1557-P10 Germany
German Research Foundation (DFG)SFB1557-P11 Germany
CitationJournal: Sci Adv / Year: 2025
Title: Mechanistic adaptation of the metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned.
Authors: Stephan Wilmes / Jesse Tönjes / Maik Drechsler / Anita Ruf / Jan-Hannes Schäfer / Anna Lürick / Dovile Januliene / Steven Apelt / Daniele Di Iorio / Seraphine V Wegner / Martin Loose / ...Authors: Stephan Wilmes / Jesse Tönjes / Maik Drechsler / Anita Ruf / Jan-Hannes Schäfer / Anna Lürick / Dovile Januliene / Steven Apelt / Daniele Di Iorio / Seraphine V Wegner / Martin Loose / Arne Moeller / Achim Paululat / Daniel Kümmel /
Abstract: Rab GTPases organize intracellular trafficking and provide identity to organelles. Their spatiotemporal activation by guanine nucleotide exchange factors (GEFs) is tightly controlled to ensure ...Rab GTPases organize intracellular trafficking and provide identity to organelles. Their spatiotemporal activation by guanine nucleotide exchange factors (GEFs) is tightly controlled to ensure fidelity. Our structural and functional comparison of the tri-longin domain RabGEFs Mon1-Ccz1 and Fuzzy-Inturned reveals the molecular basis for their target specificity. Both complexes rely on a conserved sequence motif of their substrate GTPases for the catalytic mechanism, while secondary interactions allow discrimination between targets. We also find that dimeric Mon1-Ccz1 from fungi and the metazoan homologs with the additional third subunit RMC1/Bulli bind membranes through electrostatic interactions via distinct interfaces. Protein-lipid interaction studies and functional characterization in flies reveal an essential function of RMC1/Bulli as mediator of GEF complex membrane recruitment. In the case of Fuzzy-Inturned, reconstitution experiments demonstrate that the BAR (Bin-Amphiphysin-Rvs) domain protein CiBAR1 can support membrane recruitment of the GEF. Collectively, our study demonstrates the molecular basis for the adaptation of TLD-RabGEFs to different cellular functions.
History
DepositionJun 30, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54212.png

Downloads & links

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Map

FileDownload / File: emd_54212.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 440 pix.
= 299.2 Å		0.68 Å/pix.
x 440 pix.
= 299.2 Å		0.68 Å/pix.
x 440 pix.
= 299.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0559
Minimum - Maximum-0.15418492 - 0.30810615
Average (Standard dev.)-0.00013428486 (±0.005776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 299.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54212_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54212_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of nucleotide free Ypt7 with its GEF Mon1-Ccz1

EntireName: Complex of nucleotide free Ypt7 with its GEF Mon1-Ccz1
Components
  • Complex: Complex of nucleotide free Ypt7 with its GEF Mon1-Ccz1
    • Protein or peptide: Rab small monomeric GTPase-like protein
    • Protein or peptide: Vacuolar fusion protein MON1
    • Protein or peptide: CCZ1/INTU/HSP4 first Longin domain-containing protein

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Supramolecule #1: Complex of nucleotide free Ypt7 with its GEF Mon1-Ccz1

SupramoleculeName: Complex of nucleotide free Ypt7 with its GEF Mon1-Ccz1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermochaetoides thermophila (fungus)

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Macromolecule #1: Rab small monomeric GTPase-like protein

MacromoleculeName: Rab small monomeric GTPase-like protein / type: protein_or_peptide / ID: 1 / Details: nucleotide free variant N125I / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 23.218189 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMSSRKKVL LKVIILGDSG VGKTSLMNQY VNKKFSASYK ATIGADFLTR EVMVDDRQVT MQLWDTAGQE RFQSLGVAFY RGADCCVLV FDVNNAKSFD ALDSWRDEFL IQASPRDPEN FPFVVLGIKI DVEESKRVIS TKRAQTFCQS KGGIPYFETS A KEAINVEE ...String:
GSMSSRKKVL LKVIILGDSG VGKTSLMNQY VNKKFSASYK ATIGADFLTR EVMVDDRQVT MQLWDTAGQE RFQSLGVAFY RGADCCVLV FDVNNAKSFD ALDSWRDEFL IQASPRDPEN FPFVVLGIKI DVEESKRVIS TKRAQTFCQS KGGIPYFETS A KEAINVEE AFQVIARNAL MQEESEEFSG DFQDPINIHI ENERDGCAC

UniProtKB: Rab small monomeric GTPase-like protein

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Macromolecule #2: Vacuolar fusion protein MON1

MacromoleculeName: Vacuolar fusion protein MON1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 72.198766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSMTQNN APESVAAEGT VAGQQTDTTK PEPSSQPAPE PPSQVTTDFP PNNKPNDVPA TEPASSSPRP TEPPAPPPPK PTIALSPLD IATLTFPDGT RGTFPAPPQT SAQSVSTPSI ASGHVTPQRD TDTASITSVA GTLRGVTGTA GDLASLLAGD G LGRKSKAW ...String:
GPLGSMTQNN APESVAAEGT VAGQQTDTTK PEPSSQPAPE PPSQVTTDFP PNNKPNDVPA TEPASSSPRP TEPPAPPPPK PTIALSPLD IATLTFPDGT RGTFPAPPQT SAQSVSTPSI ASGHVTPQRD TDTASITSVA GTLRGVTGTA GDLASLLAGD G LGRKSKAW RVLRAQQQAC GEGSGEEGEI TEIEGLGLGE GMEGFERELD NIPDTLPDDE RLALWKGKLK HYLILSSAGK PI WSRHGDL SLVNSTMGVV QTIISFYEGA RNPLLGFTAG KVRFVILIKG PLYFVAISRL RESDAQLRAQ LEALYMQILS TLT LPILTN IFAHRPSTDL RGPLQGTESL LASLADSFTK GSPSTLLSAL ECLRLRKSQR QAITNIFLKS RCEELLYGLL VAGG KLVSV IRPRKHSLHP SDLQLIFNML FESGGIKGNG GENWIPLCLP AFNNTGYLYM YVSFLDDKAP DDQNQPPESS NLDAS NKNS SNTPDDDLTA LILISPSREA FYALQSMRTR LVSQLLSTGY LSLIRSTALS GRPSITSILP KTPLLHFLYK SRPNVQ WCM SSLSSLTPPG ATATETLLAR RKLMSVYEEL HAALHARHAH LRVVYSTADE KEGEGLACLG WSTPAFEVYC VAPGCVG RA GMAREVNRVV QWARREEERL FILGGGVF

UniProtKB: Vacuolar fusion protein MON1

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Macromolecule #3: CCZ1/INTU/HSP4 first Longin domain-containing protein

MacromoleculeName: CCZ1/INTU/HSP4 first Longin domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Molecular weightTheoretical: 75.867539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMTTPVSPSP SGIIPAQLGF LAIYNPALGT TDETLEDQIV YYATASTLSQ ARRRHRRPRR RDRQRAQSVV KDSRPNAAGA TGDSEAVAE DKDPVSKEER HERLRQIGLA QGMVEFAKSF SDGEPVDTID TEKARVILVE VEEGWWILAS IDLTRLPLPQ I KTPTSSSA ...String:
SMTTPVSPSP SGIIPAQLGF LAIYNPALGT TDETLEDQIV YYATASTLSQ ARRRHRRPRR RDRQRAQSVV KDSRPNAAGA TGDSEAVAE DKDPVSKEER HERLRQIGLA QGMVEFAKSF SDGEPVDTID TEKARVILVE VEEGWWILAS IDLTRLPLPQ I KTPTSSSA PPPAPNLNPL PPEPAYEYSS REVKPPSLLR ADLLRAYDLF LLHHGSSLSS LLASQGRAQL VASLTRFWDH FL ATWNVLL HGNPACDVFG GIKLAASGEL GIGVGEEERG SGEREVLEGL VERVEGLVDV VVGRYGGPPS EKGPEEEQWL GLG GEVGEE DGAVFLGVGA LDRKSLRGVV QWMEEVYVWG ENAFGKPRRD LSTGHFLLGL SECSEEELTS SQANPKAIFV ELKP SYQHP SRKIPPEDPQ PLGKVGPELP RDHTARLRPV IYVSQPFIYI LLFSEITPSP STWPTLAESL HAQLSPLQKP LLHST SYRP ERPVVETTSS SGTTTQHQIF DLVYDTETLT LQSTIPNIPD PFPYSATTPT GHSTGQQHHQ QSIWTRVEAL QTHAQI LAI LSSGRAIPTD PSSFTHLPWE EGERTCKTAR GWWIVWTRVV EHSPPDAVSL HHARDDDDND DDASCSVLGH LRSVSSS HA AGSTSSSSGS GFGLGAIPGL GGLGGWAADG ATRLAQGIGI DTRRYVEGLL TSLGR

UniProtKB: CCZ1/INTU/HSP4 first Longin domain-containing protein, CCZ1/INTU/HSP4 first Longin domain-containing protein

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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

Concentration0.8 mg/mL
BufferpH: 7.3
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 524738
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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