5CX3

Crystal structure of FYCO1 LIR in complex with LC3A

  • Classification: PROTEIN BINDING
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-07-28 Released: 2016-08-03 
  • Deposition Author(s): Cheng, X., Pan, L.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), National Basic Research Program of China (973 Program)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis of FYCO1 and MAP1LC3A interaction reveals a novel binding mode for Atg8-family proteins.

Cheng, X.Wang, Y.Gong, Y.Li, F.Guo, Y.Hu, S.Liu, J.Pan, L.

(2016) Autophagy 12: 1330-1339

  • DOI: https://doi.org/10.1080/15548627.2016.1185590
  • Primary Citation of Related Structures:  
    5CX3

  • PubMed Abstract: 

    FYCO1 (FYVE and coiled-coil domain containing 1) functions as an autophagy adaptor in directly linking autophagosomes with the microtubule-based kinesin motor, and plays an essential role in the microtubule plus end-directed transport of autophagic vesicles. The specific association of FYCO1 with autophagosomes is mediated by its interaction with Atg8-family proteins decorated on the outer surface of autophagosome. However, the mechanistic basis governing the interaction between FYCO1 and Atg8-family proteins is largely unknown. Here, using biochemical and structural analyses, we demonstrated that FYCO1 contains a unique LC3-interacting region (LIR), which discriminately binds to mammalian Atg8 orthologs and preferentially binds to the MAP1LC3A and MAP1LC3B. In addition to uncovering the detailed molecular mechanism underlying the FYCO1 LIR and MAP1LC3A interaction, the determined FYCO1-LIR-MAP1LC3A complex structure also reveals a unique LIR binding mode for Atg8-family proteins, and demonstrates, first, the functional relevance of adjacent sequences C-terminal to the LIR core motif for binding to Atg8-family proteins. Taken together, our findings not only provide new mechanistic insight into FYCO1-mediated transport of autophagosomes, but also expand our understanding of the interaction modes between LIR motifs and Atg8-family proteins in general.


  • Organizational Affiliation

    a State Key Laboratory of Biorganic and Natural Products Chemistry , Shanghai , China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microtubule-associated proteins 1A/1B light chain 3A
A, B, C, D
121Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H492 (Homo sapiens)
Explore Q9H492 
Go to UniProtKB:  Q9H492
PHAROS:  Q9H492
GTEx:  ENSG00000101460 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H492
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
FYVE and coiled-coil domain-containing protein 1
E, F, G, H
31Homo sapiensMutation(s): 0 
Gene Names: FYCO1ZFYVE7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQS8 (Homo sapiens)
Explore Q9BQS8 
Go to UniProtKB:  Q9BQS8
PHAROS:  Q9BQS8
GTEx:  ENSG00000163820 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BQS8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.426α = 90
b = 115.257β = 102.29
c = 73.517γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31470749
National Basic Research Program of China (973 Program)China2013CB836900

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references, Structure summary
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references