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- PDB-9rs7: Ypt7 in complex with its GEF Mon1-Ccz1 -

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Basic information

Entry
Database: PDB / ID: 9rs7
TitleYpt7 in complex with its GEF Mon1-Ccz1
Components
  • CCZ1/INTU/HSP4 first Longin domain-containing protein
  • Rab small monomeric GTPase-like protein
  • Vacuolar fusion protein MON1
KeywordsCYTOSOLIC PROTEIN / longin domain / GEF / nucleotide exchange / endosome / autophagosome / small GTPase
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWilmes, S. / Schaefer, J. / Moeller, A. / Kuemmel, D.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1557-P10 Germany
German Research Foundation (DFG)SFB1557-P11 Germany
CitationJournal: To Be Published
Title: Mechanistic Adaptation of the Metazoan RabGEFs Mon1-Ccz1 and Fuzzy-Inturned
Authors: Wilmes, S. / Toenjes, J. / Drechsler, M. / Ruf, A. / Schaefer, J. / Luerick, A. / Januliene, D. / Apelt, S. / Di Iorio, D. / Wegner, S.V. / Loose, M. / Moeller, A. / Paululat, A. / Kuemmel, D.
History
DepositionJun 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Rab small monomeric GTPase-like protein
A: Vacuolar fusion protein MON1
B: CCZ1/INTU/HSP4 first Longin domain-containing protein


Theoretical massNumber of molelcules
Total (without water)171,2843
Polymers171,2843
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Rab small monomeric GTPase-like protein


Mass: 23218.189 Da / Num. of mol.: 1 / Mutation: N125I
Source method: isolated from a genetically manipulated source
Details: nucleotide free variant N125I / Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0065990 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGE1
#2: Protein Vacuolar fusion protein MON1


Mass: 72198.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0067370 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SGS3
#3: Protein CCZ1/INTU/HSP4 first Longin domain-containing protein


Mass: 75867.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Gene: CTHT_0050970 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SD94
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: Complex of nucleotide free Ypt7 with its GEF Mon1-Ccz1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.3
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 524738 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0038426
ELECTRON MICROSCOPYf_angle_d0.57211416
ELECTRON MICROSCOPYf_dihedral_angle_d4.0111139
ELECTRON MICROSCOPYf_chiral_restr0.0431298
ELECTRON MICROSCOPYf_plane_restr0.0041448

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