2FID | pdb_00002fid

Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb2FID/pdb

• Classification: PROTEIN TURNOVER/ENDOCYTOSIS
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-12-29 Released: 2006-02-07 
• Deposition Author(s): Lee, S., Hurley, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.268 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5

Lee, S., Tsai, Y.C., Mattera, R., Smith, W.J., Kostelansky, M.S., Weissman, A.M., Bonifacino, J.S., Hurley, J.H.

(2006) Nat Struct Mol Biol 13: 264-271

• PubMed: 16462746 
• DOI: https://doi.org/10.1038/nsmb1064
• Primary Citation Related Structures: 
  2FID, 2FIF


• PubMed Abstract: 
  

  Rabex-5 is an exchange factor for Rab5, a master regulator of endosomal trafficking. Rabex-5 binds monoubiquitin, undergoes covalent ubiquitination and contains an intrinsic ubiquitin ligase activity, all of which require an N-terminal A20 zinc finger followed immediately by a helix. The structure of the N-terminal portion of Rabex-5 bound to ubiquitin at 2.5-A resolution shows that Rabex-5-ubiquitin interactions occur at two sites. The first site is a new type of ubiquitin-binding domain, an inverted ubiquitin-interacting motif, which binds with approximately 29-microM affinity to the canonical Ile44 hydrophobic patch on ubiquitin. The second is a diaromatic patch on the A20 zinc finger, which binds with approximately 22-microM affinity to a polar region centered on Asp58 of ubiquitin. The A20 zinc-finger diaromatic patch mediates ubiquitin-ligase activity by directly recruiting a ubiquitin-loaded ubiquitin-conjugating enzyme.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, US National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.77 kDa 
• Atom Count: 1,089 
• Modeled Residue Count: 133 
• Deposited Residue Count: 146 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P0CH28 (Bos taurus) Explore P0CH28  Go to UniProtKB:  P0CH28

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rab5 GDP/GTP exchange factor	B	70	Bos taurus	Mutation(s): 0  Gene Names: RABGEF1, RABEX5
UniProt
Find proteins for O18973 (Bos taurus) Explore O18973  Go to UniProtKB:  O18973

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.268 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.967	α = 90
b = 81.967	β = 90
c = 54.443	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-02-07 
Deposition Author(s): Lee, S., Hurley, J.H.

Revision History  

• Version 1.0: 2006-02-07
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations