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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1073/pnas.2008030117
  • Structures With Same Primary Citation

  • 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. ...

    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

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-7aB184Homo sapiensMutation(s): 1 
Gene Names: RAB7ARAB7
Find proteins for P51149 (Homo sapiens)
Explore P51149 
Go to UniProtKB:  P51149
NIH Common Fund Data Resources
PHAROS  P51149
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Run domain Beclin-1-interacting and cysteine-rich domain-containing proteinA254Homo sapiensMutation(s): 0 
Gene Names: RUBCNKIAA0226
Find proteins for Q92622 (Homo sapiens)
Explore Q92622 
Go to UniProtKB:  Q92622
NIH Common Fund Data Resources
PHAROS  Q92622
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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



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 

  • 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