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- PDB-8jbe: CryoEM Structure of metazoan Mon1-Ccz1-RMC1 complex -

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Basic information

Entry
Database: PDB / ID: 8jbe
TitleCryoEM Structure of metazoan Mon1-Ccz1-RMC1 complex
Components
  • Caffeine, calcium, zinc sensitivity 1
  • MIP05619p
  • Vacuolar fusion protein MON1 homolog
KeywordsSIGNALING PROTEIN / Rab cascade / Rab GTPase / guanine nucleotide exchange factors / autophagy / Cryo-EM
Function / homology
Function and homology information


guanyl nucleotide exchange factor inhibitor activity / Mon1-Ccz1 complex / RAB GEFs exchange GTP for GDP on RABs / guanyl-nucleotide exchange factor adaptor activity / protein targeting to vacuole / endosome to lysosome transport via multivesicular body sorting pathway / neuromuscular junction development / synaptic cleft / vesicle-mediated transport / guanyl-nucleotide exchange factor activity ...guanyl nucleotide exchange factor inhibitor activity / Mon1-Ccz1 complex / RAB GEFs exchange GTP for GDP on RABs / guanyl-nucleotide exchange factor adaptor activity / protein targeting to vacuole / endosome to lysosome transport via multivesicular body sorting pathway / neuromuscular junction development / synaptic cleft / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / autophagy / late endosome membrane / regulation of autophagy / intracellular membrane-bounded organelle / lipid binding / cytosol
Similarity search - Function
Regulator of MON1-CCZ1 complex, C-terminal / Regulator of MON1-CCZ1 complex / : / Regulator of MON1-CCZ1 complex, C-terminal / Regulator of MON1-CCZ1 complex, N-terminal / Vacuolar fusion protein Ccz1 / Vacuolar fusion protein Mon1 / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 ...Regulator of MON1-CCZ1 complex, C-terminal / Regulator of MON1-CCZ1 complex / : / Regulator of MON1-CCZ1 complex, C-terminal / Regulator of MON1-CCZ1 complex, N-terminal / Vacuolar fusion protein Ccz1 / Vacuolar fusion protein Mon1 / CCZ1/INTU, second Longin domain / CCZ1/INTU/HPS4, third Longin domain / Intu longin-like domain 2 / Intu longin-like domain 3 / 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
Similarity search - Domain/homology
Regulator of MON1-CCZ1 complex / Vacuolar fusion protein MON1 homolog / Vacuolar fusion protein CCZ1 homolog
Similarity search - Component
Biological speciesDrosophila (fruit flies)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsJia, G.W. / Yong, X. / Su, Z.M. / Jia, D.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32222040 China
National Natural Science Foundation of China (NSFC)32070049 China
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
CitationJournal: To Be Published
Title: CryoEM Structure of metazoan Mon1-Ccz1-RMC1 complex
Authors: Jia, G.W. / Yong, X. / Su, Z.M. / Jia, D.
History
DepositionMay 8, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 8, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 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: MIP05619p
B: Caffeine, calcium, zinc sensitivity 1
C: Vacuolar fusion protein MON1 homolog


Theoretical massNumber of molelcules
Total (without water)189,9873
Polymers189,9873
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein MIP05619p / RMC1


Mass: 72058.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila (fruit flies) / Gene: CG8270-RA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: C0HDN5
#2: Protein Caffeine, calcium, zinc sensitivity 1 / RH02365p


Mass: 55589.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila (fruit flies)
Gene: Ccz1, C7orf28B, Dccz1, Dmel\CG14980, NP_647835, CG14980, Dmel_CG14980
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9VZL5
#3: Protein Vacuolar fusion protein MON1 homolog


Mass: 62338.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila (fruit flies)
Gene: Mon1, Dmel\CG11926, Dmon1, dMon1, MON1, mon1, Mon1-RA, NP_608868, CG11926, Dmel_CG11926
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9VR38
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: CryoEM structure of the metazoan Mon1-Ccz1-RMC1 complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Drosophila (fruit flies)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 63 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111235 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311485
ELECTRON MICROSCOPYf_angle_d0.53815536
ELECTRON MICROSCOPYf_dihedral_angle_d4.1131507
ELECTRON MICROSCOPYf_chiral_restr0.0431787
ELECTRON MICROSCOPYf_plane_restr0.0041965

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