ISDA

Deposition Date 2020-03-31

Release Date 2020-07-01

Last Version Date 2023-10-18

Entry Detail

PDB ID:

6WCW

Keywords:

METAL BINDING PROTEIN

Title:

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

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli BL21

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.80 Å

R-Value Free:

0.25

R-Value Work:

0.19

R-Value Observed:

0.20

Space Group:

I 1 2 1

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Run domain Beclin-1-interacting and cysteine-rich domain-containing protein
Gene (Uniprot):RUBCN
Chain IDs:B (auth: A)
Chain Length:254
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q92622 Pfam ID:PF13901

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ras-related protein Rab-7a
Gene (Uniprot):RAB7A
Mutations:Q67L
Chain IDs:A (auth: B)
Chain Length:184
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:P51149 Pfam ID:PF00071

Ligand Molecules

GTP

Primary Citation

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.Show

Proc.Natl.Acad.Sci.USA 117 17003 17010 (2020)

PMID: 32632011 DOI: 10.1073/pnas.2008030117

Abstact

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.

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Primary Citation of related structures