4XI7

Crystal structure of the MZM-REP domains of Mind bomb 1 in complex with Jagged1 N-box peptide

  • Classification: LIGASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2015-01-06 Released: 2015-03-18 
  • Deposition Author(s): McMillan, B.J., Blacklow, S.C.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute; American Cancer Society; German Research Foundation 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.051 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase MIB1
A
380Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Jagged 1 N-box peptide
C
11Homo sapiensMutation(s): 0 
Gene Names: JAG1 (JAGL1)
Find proteins for P78504 (Homo sapiens)
Go to Gene View: JAG1
Go to UniProtKB:  P78504
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.051 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 73.728α = 90.00
b = 73.728β = 90.00
c = 170.276γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHENIXphasing
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesP01 CA119070
American Cancer SocietyUnited States120246-PF-11-044-01-DMC
German Research FoundationGermanyKL 1028/3-1

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence