5V4K

Crystal structure of NEDD4 LIR-fused human LC3B_2-119


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into links between autophagy and the ubiquitin system from the structure of LC3B bound to the LIR motif from the E3 ligase NEDD4.

Qiu, Y.Zheng, Y.Wu, K.P.Schulman, B.A.

(2017) Protein Sci. 26: 1674-1680

  • DOI: 10.1002/pro.3186

  • PubMed Abstract: 
  • Members of the LC3/GABARAP family of ubiquitin-like proteins function during autophagy by serving as membrane linked protein-binding platforms. Their C-termini are physically attached to membranes through covalent linkage to primary amines on lipids ...

    Members of the LC3/GABARAP family of ubiquitin-like proteins function during autophagy by serving as membrane linked protein-binding platforms. Their C-termini are physically attached to membranes through covalent linkage to primary amines on lipids such as phosphatidylethanolamine, while their ubiquitin-like fold domains bind "LIR" (LC3-Interacting Region) sequences found within an extraordinarily diverse array of proteins including regulators of autophagy, adaptors that recruit ubiquitinated cargoes to be degraded, and even proteins controlling processes at membranes that are not associated with autophagy. Recently, LC3/GABARAP proteins were found to bind the ubiquitin E3 ligase NEDD4 to influence ubiquitination associated with autophagy in human cell lines. Here, we use purified recombinant proteins to define LC3B interactions with a specific LIR sequence from NEDD4, present a crystal structure showing atomic details of the interaction, and show that LC3B-binding can steer intrinsic NEDD4 E3 ligase activity. The data provide detailed molecular insights underlying recruitment of an E3 ubiquitin ligase to phagophores during autophagy.


    Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105.,Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, Tennessee, 38105.,Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, 38103.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microtubule-associated proteins 1A/1B light chain 3B,Microtubule-associated proteins 1A/1B light chain 3B,Microtubule-associated proteins 1A/1B light chain 3B
A, B
132Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3B (MAP1ALC3)
Find proteins for Q9GZQ8 (Homo sapiens)
Go to Gene View: MAP1LC3B
Go to UniProtKB:  Q9GZQ8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.182 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.570α = 90.00
b = 69.570β = 90.00
c = 119.620γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-08-02
    Type: Author supporting evidence, Database references