Related Experiment Video

Updated: Jul 10, 2025

Two- and Three-Dimensional Live Cell Imaging of DNA Damage Response Proteins
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Two- and Three-Dimensional Live Cell Imaging of DNA Damage Response Proteins

Published on: September 28, 2012

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Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation

Ming Liu1, Yang Wang1, Fei Teng1,2

  • 1Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, 518172, China.

Nature Communications
|November 22, 2023
PubMed

Insights

AMBRA1, a tumor suppressor, is structurally characterized through cryo-EM, revealing its complex with DDB1. This interaction stabilizes AMBRA1, impacting cell cycle regulation and substrate ubiquitination.

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • AMBRA1 is a tumor suppressor protein involved in autophagy and cell cycle regulation.
  • Its intrinsic disorder has hindered previous structural determination.
  • AMBRA1 functions as a substrate receptor in the ubiquitin conjugation system.

Purpose of the Study:

  • To determine the structure of AMBRA1 in complex with DDB1.
  • To elucidate the mechanism of AMBRA1 stabilization and substrate recruitment.
  • To understand AMBRA1's role in the ubiquitin ligase complex.

Main Methods:

  • Hydrogen deuterium exchange mass spectrometry (HDX-MS) to analyze protein dynamics.
  • Cryo-electron microscopy (cryo-EM) to determine the structure of the AMBRA1-DDB1 complex.
  • In vitro ubiquitination assays using AMBRA1 mutants.

Main Results:

  • HDX-MS revealed AMBRA1 as a highly flexible protein, stabilized by DDB1 binding.
  • The cryo-EM structure (3.08 Å resolution) shows DDB1 engaging with AMBRA1's WD40 domain.
  • DDB1 binding-defective AMBRA1 mutants impair Cyclin D1 ubiquitination and accelerate cell cycle progression.

Conclusions:

  • Structural insights into the AMBRA1-DDB1 complex provide a mechanism for substrate recruitment.
  • AMBRA1 acts as a crucial hub in various physiological processes via ubiquitin ligase complex interaction.
  • The findings clarify AMBRA1's role in cell cycle regulation through targeted protein ubiquitination.

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