Non-covalent assembly of monoubiquitin that mimics K11 poly-ubiquitin

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Tetrameric Assembly of Monoubiquitin Accurately Mimics the Lys11 Polyubiquitin Chain Structure.

Levin-Kravets, O.Shohat, N.Prag, G.

(2015) Biochemistry 54: 4704-4710

  • DOI: https://doi.org/10.1021/acs.biochem.5b00498
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Specific lysine residues on the ubiquitin surface were selected during the course of evolution to form different polyubiquitin chain structures that signal diverse cellular processes. A vast number of ubiquitin receptors specifically recognize and decode the signals conferred by these polyubiquitin chains. The mechanisms of formation and the structure of Lys11-linked ubiquitin, which signals for cell-cycle and innate immune control, have been elucidated. Here, we present a new crystal structure of monomeric ubiquitin that accurately mimics one of the structures of Lys11-linked ubiquitin. Analysis of the ubiquitin:ubiquitin interface demonstrates structural fitness and specificity. The interaction is exclusively hydrophilic, leaving the Ile44 hydrophobic patch, a major recognition site for ubiquitin receptors, exposed. These noncovalent ubiquitin:ubiquitin interactions are nearly identical to those reported for Lys11-linked ubiquitin and seem to play a significant role in stabilizing the crystal structure without the isopeptide bond. In vitro cross-linking analysis with wild-type ubiquitin or its mutants partially mimics the interactions in the crystal. We suggest that these interactions may play a biological role in transmitting Lys11-linked ubiquitin chain-type cellular signals.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology and Institute for Structural Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27a
A, B, C, D
76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P62992 (Bos taurus)
Explore P62992 
Go to UniProtKB:  P62992
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62992
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MLA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
K [auth B]
N [auth C]
O [auth C]
E [auth A],
F [auth A],
K [auth B],
N [auth C],
O [auth C],
R [auth D]
C3 H4 O4
Query on SCN

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
L [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
S [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.319α = 90
b = 81.301β = 129.33
c = 58.597γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Israeli Science Foundation464/11

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2015-08-12
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description