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- PDB-9l0d: Cryo-EM structure of the human MON1A/CCZ1/C18orf8 complex -

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Basic information

Entry
Database: PDB / ID: 9l0d
TitleCryo-EM structure of the human MON1A/CCZ1/C18orf8 complex
Components
  • Ras-related protein Rab-7a
  • Regulator of MON1-CCZ1 complex
  • Vacuolar fusion protein CCZ1 homolog B
  • Vacuolar fusion protein MON1 homolog A
KeywordsSIGNALING PROTEIN / MON1A / CCZ1 / C18orf8 / Rab7A / autophagy
Function / homology
Function and homology information


Mon1-Ccz1 complex / synaptic vesicle recycling via endosome / lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / neurotransmitter receptor transport, postsynaptic endosome to lysosome / epidermal growth factor catabolic process / alveolar lamellar body / negative regulation of intralumenal vesicle formation ...Mon1-Ccz1 complex / synaptic vesicle recycling via endosome / lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / neurotransmitter receptor transport, postsynaptic endosome to lysosome / epidermal growth factor catabolic process / alveolar lamellar body / negative regulation of intralumenal vesicle formation / Suppression of autophagy / phagosome-lysosome fusion / negative regulation of exosomal secretion / establishment of vesicle localization / retromer complex binding / phagosome maturation / presynaptic endosome / protein localization to lysosome / endosome to plasma membrane protein transport / early endosome to late endosome transport / phagophore assembly site membrane / positive regulation of exosomal secretion / protein targeting to vacuole / RAB geranylgeranylation / protein targeting to lysosome / melanosome membrane / RAB GEFs exchange GTP for GDP on RABs / RHOD GTPase cycle / RHOF GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / autophagosome membrane / viral release from host cell / protein secretion / RHOH GTPase cycle / RHOG GTPase cycle / autophagosome assembly / RAC2 GTPase cycle / RAC3 GTPase cycle / bone resorption / intracellular transport / lipid catabolic process / vesicle-mediated transport / phagocytic vesicle / lipid droplet / RAC1 GTPase cycle / Prevention of phagosomal-lysosomal fusion / MHC class II antigen presentation / secretory granule membrane / guanyl-nucleotide exchange factor activity / small monomeric GTPase / response to bacterium / autophagy / small GTPase binding / mitochondrial membrane / phagocytic vesicle membrane / endocytosis / positive regulation of protein catabolic process / GDP binding / synaptic vesicle membrane / late endosome membrane / late endosome / protein transport / G protein activity / lysosome / endosome membrane / regulation of autophagy / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / Neutrophil degranulation / GTP binding / glutamatergic synapse / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / 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 / 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 / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ras-related protein Rab-7a / Vacuolar fusion protein CCZ1 homolog B / Vacuolar fusion protein MON1 homolog A / Regulator of MON1-CCZ1 complex
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsTang, Y. / Han, Y. / Zhang, Y. / Pan, L.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022ZD0207400 China
National Natural Science Foundation of China (NSFC)92253301 China
National Natural Science Foundation of China (NSFC)32071219 China
CitationJournal: Protein Cell / Year: 2025
Title: Mechanistic insights into the GEF activity of the human MON1A/CCZ1/C18orf8 complex.
Authors: Yubin Tang / Yaoyao Han / Zhenpeng Guo / Ying Li / Xinyu Gong / Yuchao Zhang / Haobo Liu / Xindi Zhou / Daichao Xu / Yixiao Zhang / Lifeng Pan /
History
DepositionDec 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar fusion protein MON1 homolog A
B: Vacuolar fusion protein CCZ1 homolog B
C: Regulator of MON1-CCZ1 complex
D: Ras-related protein Rab-7a


Theoretical massNumber of molelcules
Total (without water)202,0964
Polymers202,0964
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 Vacuolar fusion protein MON1 homolog A


Mass: 47562.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MON1A, SAND1 / Production host: Homo sapiens (human) / References: UniProt: Q86VX9
#2: Protein Vacuolar fusion protein CCZ1 homolog B / Vacuolar fusion protein CCZ1 homolog-like


Mass: 55935.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCZ1B, C7orf28B / Production host: Homo sapiens (human) / References: UniProt: P86790
#3: Protein Regulator of MON1-CCZ1 complex / Colon cancer-associated protein Mic1 / Mic-1 / WD repeat-containing protein 98


Mass: 75068.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RMC1, C18orf8, MIC1, WDR98 / Production host: Homo sapiens (human) / References: UniProt: Q96DM3
#4: Protein Ras-related protein Rab-7a


Mass: 23529.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB7A, RAB7 / Production host: Homo sapiens (human) / References: UniProt: P51149, small monomeric GTPase
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: MCCR complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: Tecnai Spirit / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI SPIRIT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77193 / Symmetry type: POINT

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