2C7N

Human Rabex-5 residues 1-74 in complex with Ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal Structure of the Ubiquitin Binding Domains of Rabex-5 Reveals Two Modes of Interaction with Ubiquitin.

Penengo, L., Mapelli, M., Murachelli, A.G., Confalonieri, S., Magri, L., Musacchio, A., Di Fiore, P.P., Polo, S., Schneider, T.R.

(2006) Cell 124: 1183

  • DOI: 10.1016/j.cell.2006.02.020
  • Primary Citation of Related Structures:  
    2C7M, 2C7N

  • PubMed Abstract: 

    • The interaction between ubiquitinated proteins and intracellular proteins harboring ubiquitin binding domains (UBDs) is critical to a multitude of cellular processes. Here, we report that Rabex-5, a guanine nucleotide exchange factor for Rab5, binds ...

    The interaction between ubiquitinated proteins and intracellular proteins harboring ubiquitin binding domains (UBDs) is critical to a multitude of cellular processes. Here, we report that Rabex-5, a guanine nucleotide exchange factor for Rab5, binds to Ub through two independent UBDs. These UBDs determine a number of properties of Rabex-5, including its coupled monoubiquitination and interaction in vivo with ubiquitinated EGFRs. Structural and biochemical characterization of the UBDs of Rabex-5 revealed that one of them (MIU, motif interacting with ubiquitin) binds to Ub with modes superimposable to those of the UIM (ubiquitin-interacting motif):Ub interaction, although in the opposite orientation. The other UBD, RUZ (Rabex-5 ubiquitin binding zinc finger) binds to a surface of Ub centered on Asp58(Ub) and distinct from the "canonical" Ile44(Ub)-based surface. The two binding surfaces allow Ub to interact simultaneously with different UBDs, thus opening new perspectives in Ub-mediated signaling.

    Organizational Affiliation: 

    IFOM, the FIRC Institute for Molecular Oncology Foundation, Via Adamello 16, 20139 Milan, Italy.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1A, C, E, G, I, K74Homo sapiensMutation(s): 0 
Gene Names: RABGEF1, RABEX5
Find proteins for Q9UJ41 (Homo sapiens)
Explore Q9UJ41 
Go to UniProtKB:  Q9UJ41
NIH Common Fund Data Resources
PHAROS  Q9UJ41
GTEx  ENSG00000154710
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UBIQUITINB, D, F, H, J, L76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P0CH28 (Bos taurus)
Explore P0CH28 
Go to UniProtKB:  P0CH28
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download CCD File 
A, C, E, G, I, K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.3α = 108.2
b = 68.9β = 102.7
c = 98.5γ = 90.4
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
HKL2MAPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other