Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, immunoprecipitation, microscopy

Macromolecule Content

• Total Structure Weight: 51.19 kDa 
• Atom Count: 3,447 
• Modelled Residue Count: 423 
• Deposited Residue Count: 438 
• Unique protein chains: 2

 6WCW

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

• PDB DOI:  https://doi.org/10.2210/pdb6WCW/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2020-03-31 Released: 2020-07-01 
• Deposition Author(s): Bhargava, H.K., Byck, J.M., Farrell, D.P., Anishchenko, I., DiMaio, F., Im, Y.J., Hurley, J.H.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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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 

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

• PubMed: 32632011 
• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-7a	A [auth B]	184	Homo sapiens	Mutation(s): 1  Gene Names: RAB7A, RAB7 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Run domain Beclin-1-interacting and cysteine-rich domain-containing protein	B [auth A]	254	Homo sapiens	Mutation(s): 0  Gene Names: RUBCN, KIAA0226
UniProt & NIH Common Fund Data Resources
Find proteins for Q92622 (Homo sapiens) Explore Q92622  Go to UniProtKB:  Q92622
PHAROS:  Q92622

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	C [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN	E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 60.04	α = 90
b = 45.33	β = 98.507
c = 186.277	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
ELVES	data processing
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-01 
Deposition Author(s): Bhargava, H.K., Byck, J.M., Farrell, D.P., Anishchenko, I., DiMaio, F., Im, Y.J., Hurley, J.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM123089
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 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