1BT0

STRUCTURE OF UBIQUITIN-LIKE PROTEIN, RUB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The rub family of ubiquitin-like proteins. Crystal structure of Arabidopsis rub1 and expression of multiple rubs in Arabidopsis.

Rao-Naik, C.delaCruz, W.Laplaza, J.M.Tan, S.Callis, J.Fisher, A.J.

(1998) J Biol Chem 273: 34976-34982

  • DOI: 10.1074/jbc.273.52.34976
  • Primary Citation of Related Structures:  
    1BT0

  • PubMed Abstract: 
  • Several proteins with significant identity to ubiquitin have been characterized recently. In contrast to ubiquitin's main role in targeting proteins for degradation, a described function of one family of ubiquitin-related proteins, the Rub family, is ...

    Several proteins with significant identity to ubiquitin have been characterized recently. In contrast to ubiquitin's main role in targeting proteins for degradation, a described function of one family of ubiquitin-related proteins, the Rub family, is to serve as a stable post-translational modification of a complex involved in the G1-to-S cell cycle transition. Rub proteins have been found in animals, plants, and fungi and consist of 76 residues with 52-63% identity to ubiquitin. In this study three different RUB proteins within the plant Arabidopsis are identified; two differ by only 1 amino acid, while the third is only 77.6% identical to the other two. Genes encoding all three are expressed in multiple organs. In addition, we report the crystal structure of higher plant RUB1 at 1.7-A resolution to help elucidate the functional differences between Rub and ubiquitin. RUB1 contains a single globular domain with a flexible COOH-terminal extension. The overall RUB1 structure is very similar to ubiquitin. The majority of the amino acid differences between RUB1 and ubiquitin map to the surface. These changes alter the electrostatic surface potential in two regions and likely confer specificity between ubiquitin and RUB1 and their ubiquitin-activating enzyme (E1) or E1-like activating enzymes.


    Related Citations: 
    • Structure of Ubiquitin Refined at 1.8 Angstroms Resolution
      Vijay-Kumar, S., Bugg, C.E., Cook, W.J.
      (1987) J Mol Biol 194: 531

    Organizational Affiliation

    Section of Molecular and Cellular Biology, University of California, Davis, California 95616, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (UBIQUITIN-LIKE PROTEIN 7, RUB1)A76Arabidopsis thalianaMutation(s): 3 
Gene Names: RUB1NEDD8UBQ15At1g31340T19E23.13
Find proteins for Q9SHE7 (Arabidopsis thaliana)
Explore Q9SHE7 
Go to UniProtKB:  Q9SHE7
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.6α = 90
b = 35.6β = 102.8
c = 37.9γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
XDSdata reduction
CCP4data scaling
ROTAVATAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-12-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description