3NOB

Structure of K11-linked di-ubiquitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


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

Literature

K11-Linked Polyubiquitination in Cell Cycle Control Revealed by a K11 Linkage-Specific Antibody.

Matsumoto, M.L., Wickliffe, K.E., Dong, K.C., Yu, C., Bosanac, I., Bustos, D., Phu, L., Kirkpatrick, D.S., Hymowitz, S.G., Rape, M., Kelley, R.F., Dixit, V.M.

(2010) Mol.Cell 39: 477-484

  • DOI: 10.1016/j.molcel.2010.07.001

  • PubMed Abstract: 

    • Polyubiquitination is a posttranslational modification where ubiquitin chains containing isopeptide bonds linking one of seven ubiquitin lysines with the C terminus of an adjoining ubiquitin are covalently attached to proteins. While functions of K48 ...

    Polyubiquitination is a posttranslational modification where ubiquitin chains containing isopeptide bonds linking one of seven ubiquitin lysines with the C terminus of an adjoining ubiquitin are covalently attached to proteins. While functions of K48- and K63-linked polyubiquitin are understood, the role(s) of noncanonical K11-linked chains is less clear. A crystal structure of K11-linked diubiquitin demonstrates a distinct conformation from K48- or K63-linked diubiquitin. We engineered a K11 linkage-specific antibody and use it to demonstrate that K11 chains are highly upregulated in mitotic human cells precisely when substrates of the ubiquitin ligase anaphase-promoting complex (APC/C) are degraded. These chains increased with proteasomal inhibition, suggesting they act as degradation signals in vivo. Inhibition of the APC/C strongly impeded the formation of K11-linked chains, suggesting that a single ubiquitin ligase is the major source of mitotic K11-linked chains. Our results underscore the importance of K11-linked ubiquitin chains as critical regulators of mitotic protein degradation.

    Organizational Affiliation: 

    Department of Antibody Engineering, Genentech, Inc., South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A, B, C, D, E, F, G, H
78Homo sapiensMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B, D, E, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 155.597α = 90.00
b = 56.059β = 95.21
c = 65.772γ = 90.00
Software Package:
Software NamePurpose
BOSdata collection
PHENIXrefinement
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-04-02
    Type: Structure summary