6WCW

Structure of human Rubicon RH domain in complex with GTP-bound Rab7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex.

Bhargava, H.K.Tabata, K.Byck, J.M.Hamasaki, M.Farrell, D.P.Anishchenko, I.DiMaio, F.Im, Y.J.Yoshimori, T.Hurley, J.H.

(2020) Proc Natl Acad Sci U S A 117: 17003-17010

  • DOI: https://doi.org/10.1073/pnas.2008030117
  • Primary Citation of Related Structures:  
    6WCW

  • PubMed Abstract: 

    Rubicon is a potent negative regulator of autophagy and a potential target for autophagy-inducing therapeutics. Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP. Here we report the 2.8-Å crystal structure of the Rubicon RH domain in complex with Rab7-GTP. Our structure reveals a fold for the RH domain built around four zinc clusters. The switch regions of Rab7 insert into pockets on the surface of the RH domain in a mode that is distinct from those of other Rab-effector complexes. Rubicon residues at the dimer interface are required for Rubicon and Rab7 to colocalize in living cells. Mutation of Rubicon RH residues in the Rab7-binding site restores efficient autophagic flux in the presence of overexpressed Rubicon, validating the Rubicon RH domain as a promising therapeutic target.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-7aA [auth B]184Homo sapiensMutation(s): 1 
Gene Names: RAB7ARAB7
UniProt & NIH Common Fund Data Resources
Find proteins for P51149 (Homo sapiens)
Explore P51149 
Go to UniProtKB:  P51149
GTEx:  ENSG00000075785 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51149
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Run domain Beclin-1-interacting and cysteine-rich domain-containing proteinB [auth A]254Homo sapiensMutation(s): 0 
Gene Names: RUBCNKIAA0226
UniProt & NIH Common Fund Data Resources
Find proteins for Q92622 (Homo sapiens)
Explore Q92622 
Go to UniProtKB:  Q92622
GTEx:  ENSG00000145016 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92622
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.04α = 90
b = 45.33β = 98.507
c = 186.277γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
ELVESdata processing
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM123089
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM111730

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2020-08-05
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description