4TSE

Crystal Structure of the Mib Repeat Domain of Mind bomb 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.057 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A tail of two sites: a bipartite mechanism for recognition of notch ligands by mind bomb e3 ligases.

McMillan, B.J.Schnute, B.Ohlenhard, N.Zimmerman, B.Miles, L.Beglova, N.Klein, T.Blacklow, S.C.

(2015) Mol.Cell 57: 912-924

  • DOI: 10.1016/j.molcel.2015.01.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mind bomb (Mib) proteins are large, multi-domain E3 ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. This ubiquitination step marks the ligand proteins for epsin-dependent endocytosis, which is critical for in vivo Notch ...

    Mind bomb (Mib) proteins are large, multi-domain E3 ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. This ubiquitination step marks the ligand proteins for epsin-dependent endocytosis, which is critical for in vivo Notch receptor activation. We present here crystal structures of the substrate recognition domains of Mib1, both in isolation and in complex with peptides derived from Notch ligands. The structures, in combination with biochemical, cellular, and in vivo assays, show that Mib1 contains two independent substrate recognition domains that engage two distinct epitopes from the cytoplasmic tail of the ligand Jagged1, one in the intracellular membrane proximal region and the other near the C terminus. Together, these studies provide insights into the mechanism of ubiquitin transfer by Mind bomb E3 ligases, illuminate a key event in ligand-induced activation of Notch receptors, and identify a potential target for therapeutic modulation of Notch signal transduction in disease.


    Organizational Affiliation

    Harvard Medical School, Boston, MA 02115, USA; Dana Farber Cancer Institute, Boston, MA 02215 USA. Electronic address: Stephen_Blacklow@hms.harvard.edu.,University of Dusseldorf, Dusseldorf 40225, Germany.,Harvard Medical School, Boston, MA 02115, USA; Dana Farber Cancer Institute, Boston, MA 02215 USA.,Harvard Medical School, Boston, MA 02115, USA; Beth-Israel Deaconess Medical Center, Boston, MA, 02215 USA.,Harvard Medical School, Boston, MA 02115, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase MIB1
A, B
174Homo sapiensMutation(s): 0 
Gene Names: MIB1 (DIP1, KIAA1323, ZZANK2)
EC: 2.3.2.27
Find proteins for Q86YT6 (Homo sapiens)
Go to Gene View: MIB1
Go to UniProtKB:  Q86YT6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.057 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.320α = 90.00
b = 86.420β = 90.00
c = 86.600γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01 CA119070

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.2: 2019-12-04
    Type: Author supporting evidence