6J04

Crystal structure of full length human LC3B delta G120 mutant (2_125)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.899 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Allele-selective lowering of mutant HTT protein by HTT-LC3 linker compounds

Li, Z.Y.Wang, C.Wang, Z.Y.Zhu, C.G.Li, J.Sha, T.Ma, L.X.Gao, C.Yang, Y.Sun, Y.M.Wang, J.Sun, X.L.Lu, C.Q.Difiglia, M.Mein, Y.Ding, C.Luo, S.Q.Dang, Y.J.Ding, Y.Fei, Y.Y.Lu, B.X.

(2019) Nature 575: 203-209

  • DOI: 10.1038/s41586-019-1722-1

  • PubMed Abstract: 
  • Accumulation of mutant proteins is a major cause of many diseases (collectively called proteopathies), and lowering the level of these proteins can be useful for treatment of these diseases. We hypothesized that compounds that interact with both the ...

    Accumulation of mutant proteins is a major cause of many diseases (collectively called proteopathies), and lowering the level of these proteins can be useful for treatment of these diseases. We hypothesized that compounds that interact with both the autophagosome protein microtubule-associated protein 1A/1B light chain 3 (LC3) 1 and the disease-causing protein may target the latter for autophagic clearance. Mutant huntingtin protein (mHTT) contains an expanded polyglutamine (polyQ) tract and causes Huntington's disease, an incurable neurodegenerative disorder 2 . Here, using small-molecule-microarray-based screening, we identified four compounds that interact with both LC3 and mHTT, but not with the wild-type HTT protein. Some of these compounds targeted mHTT to autophagosomes, reduced mHTT levels in an allele-selective manner, and rescued disease-relevant phenotypes in cells and in vivo in fly and mouse models of Huntington's disease. We further show that these compounds interact with the expanded polyQ stretch and could lower the level of mutant ataxin-3 (ATXN3), another disease-causing protein with an expanded polyQ tract 3 . This study presents candidate compounds for lowering mHTT and potentially other disease-causing proteins with polyQ expansions, demonstrating the concept of lowering levels of disease-causing proteins using autophagosome-tethering compounds.


    Organizational Affiliation

    Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai, China.,Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai, China. yuding@fudan.edu.cn.,Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai, China. luboxun@fudan.edu.cn.,Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, China. fyy@fudan.edu.cn.,Large-scale Preparation System, National Facility for Protein Science in Shanghai, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, China.,Peninsula Schools of Medicine and Dentistry, Institute of Translational and Stratified Medicine, University of Plymouth, Plymouth, UK.,Laboratory of Cellular Neurobiology, Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA.,Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Department of Anatomy, Histology and Embryology, Shanghai Medical College, Fudan University, Shanghai, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microtubule-associated proteins 1A/1B light chain 3B
A, B, C, D
124Homo 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 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.899 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.644α = 99.27
b = 56.475β = 97.45
c = 67.040γ = 109.94
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (China)China31470764
National Science Foundation (China)China91527305

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Type: Database references