5YIQ

Crystal structure of AnkG LIR/LC3B complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

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:  
    5YIP, 5YIR, 5YIQ, 5YIS

  • 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 specific functions of Atg8 proteins in autophagy ...

    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 kDa ankyrin-G and a super-potent pan-Atg8 inhibitory peptide from 440 kDa 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

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Microtubule-associated proteins 1A/1B light chain 3BA125Mus musculusMutation(s): 0 
Gene Names: Map1lc3bMap1alc3Map1lc3
UniProt
Find proteins for Q9CQV6 (Mus musculus)
Explore Q9CQV6 
Go to UniProtKB:  Q9CQV6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ankyrin-3B [auth D]26Rattus norvegicusMutation(s): 0 
Gene Names: Ank3
UniProt
Find proteins for O70511 (Rattus norvegicus)
Explore O70511 
Go to UniProtKB:  O70511
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.553α = 90
b = 64.553β = 90
c = 155.461γ = 120
Software Package:
Software NamePurpose
DENZOdata collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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