5YIQ

Crystal structure of AnkG LIR/LC3B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins.

Li, J.Zhu, R.Chen, K.Zheng, H.Zhao, H.Yuan, C.Zhang, H.Wang, C.Zhang, M.

(2018) Nat. Chem. Biol. 14: 778-787

  • DOI: 10.1038/s41589-018-0082-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mammalian Atg8 family proteins are central drivers of autophagy and contain six members, classified into the LC3 and GABARAP subfamilies. Due to their high sequence similarity and consequent functional overlaps, it is difficult to delineate speci ...

    The mammalian Atg8 family proteins are central drivers of autophagy and contain six members, classified into the LC3 and GABARAP subfamilies. Due to their high sequence similarity and consequent functional overlaps, it is difficult to delineate specific functions of Atg8 proteins in autophagy. Here we discover a super-strong GABARAP-selective inhibitory peptide harbored in 270/480‚ÄČkDa ankyrin-G and a super-potent pan-Atg8 inhibitory peptide from 440‚ÄČkDa ankyrin-B. Structural studies elucidate the mechanism governing the Atg8 binding potency and selectivity of the peptides, reveal a general Atg8-binding sequence motif, and allow development of a more GABARAP-selective inhibitory peptide. These peptides effectively blocked autophagy when expressed in cultured cells. Expression of these ankyrin-derived peptides in Caenorhabditis elegans also inhibited autophagy, causing accumulation of the p62 homolog SQST-1, delayed development and shortened life span. Thus, these genetically encodable autophagy inhibitory peptides can be used to occlude autophagy spatiotemporally in living animals.


    Organizational Affiliation

    Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. cwangust@ustc.edu.cn.,Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China. cwangust@ustc.edu.cn.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. mzhang@ust.hk.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. hongzhang@sun5.ibp.ac.cn.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China. hongzhang@sun5.ibp.ac.cn.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,Center of Systems Biology and Human Health, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. mzhang@ust.hk.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microtubule-associated proteins 1A/1B light chain 3B
A
125Mus musculusMutation(s): 0 
Gene Names: Map1lc3b (Map1alc3, Map1lc3)
Find proteins for Q9CQV6 (Mus musculus)
Go to UniProtKB:  Q9CQV6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ankyrin-3
D
26Rattus norvegicusMutation(s): 0 
Gene Names: Ank3
Find proteins for O70511 (Rattus norvegicus)
Go to UniProtKB:  O70511
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 64.553α = 90.00
b = 64.553β = 90.00
c = 155.461γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata collection
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Grants Council (RGC)Hong KongAoE-M09-12

Revision History 

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-07-04
    Type: Data collection, Database references, Derived calculations
  • Version 1.2: 2018-08-01
    Type: Data collection, Database references