9LOL | pdb_00009lol

Cryo-EM structure of human MON1A-CCZ1-RAB7A


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structure of the human MON1A-CCZ1-RAB7A complex provides insights into nucleotide exchange mechanism.

Li, X.Li, D.Tang, D.Huang, X.Bao, H.Wang, J.Qi, S.

(2025) Life Metab 4: loaf017-loaf017

  • DOI: https://doi.org/10.1093/lifemeta/loaf017
  • Primary Citation of Related Structures:  
    9LOL

  • PubMed Abstract: 

    Autophagy is a fundamental cellular process, conserved across species from yeast to mammals, that plays a crucial role in maintaining cellular homeostasis. The functionally conserved MON1-CCZ1 (MC1) complex serves as a guanine nucleotide exchange factor (GEF) for the RAB GTPase RAB7A and is indispensable for directing RAB7A recruitment to autophagosome or lysosomal membranes. Despite its critical role, the precise molecular mechanism underlying the assembly of the human MON1A-CCZ1 (HsMC1) complex and its specific GEF activity towards RAB7A has remained unclear. In this study, we report the high-resolution cryo-electron microscopy (cryo-EM) structure of the HsMC1 GEF domain in a complex with the nucleotide-free RAB7A N125I at 2.85 Å resolution. Our structural data demonstrate that engagement with the HsMC1 complex induces marked conformational shifts in the phosphate-binding loop (P-loop) and Switch I/II regions of RAB7A. A striking feature of this complex is the direct interaction between the P-loop of RAB7A and CCZ1, a structural detail not previously observed. Furthermore, biochemical assays targeting residues within Interface I or II of the HsMC1-RAB7A complex highlight their critical role in mediating the interaction and suggest a unique mechanism for nucleotide exchange facilitated by the HsMC1 complex. These findings provide novel molecular insights into the functional mechanisms of the HsMC1-RAB7A complex, offering a robust structural framework to inform future investigations into disease-related targets and therapeutic development.


  • Organizational Affiliation
    • Department of Urology, Institute of Urology, State Key Laboratory of Biotherapy, West China Hospital, College of Life Sciences, Sichuan University, and National Collaborative Innovation Center, Chengdu, Sichuan 610041, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar fusion protein CCZ1 homolog B482Homo sapiensMutation(s): 0 
Gene Names: CCZ1BC7orf28B
UniProt & NIH Common Fund Data Resources
Find proteins for P86790 (Homo sapiens)
Explore P86790 
Go to UniProtKB:  P86790
GTEx:  ENSG00000146574 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP86790
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar fusion protein MON1 homolog A555Homo sapiensMutation(s): 0 
Gene Names: MON1ASAND1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VX9 (Homo sapiens)
Explore Q86VX9 
Go to UniProtKB:  Q86VX9
PHAROS:  Q86VX9
GTEx:  ENSG00000164077 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86VX9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-7a207Homo sapiensMutation(s): 1 
Gene Names: RAB7ARAB7
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P51149 (Homo sapiens)
Explore P51149 
Go to UniProtKB:  P51149
PHAROS:  P51149
GTEx:  ENSG00000075785 
Entity Groups  
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UniProt GroupP51149
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China32201025
National Science Foundation (NSF, China)China32071214
National Science Foundation (NSF, China)China32471311

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release