5CX3

Crystal structure of FYCO1 LIR in complex with LC3A

  • Classification: PROTEIN BINDING
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1080/15548627.2016.1185590

  • 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 v ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Microtubule-associated proteins 1A/1B light chain 3A
A, B, C, D
121Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3A
Find proteins for Q9H492 (Homo sapiens)
Go to Gene View: MAP1LC3A
Go to UniProtKB:  Q9H492
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FYVE and coiled-coil domain-containing protein 1
E, F, G, H
31Homo sapiensMutation(s): 0 
Gene Names: FYCO1 (ZFYVE7)
Find proteins for Q9BQS8 (Homo sapiens)
Go to Gene View: FYCO1
Go to UniProtKB:  Q9BQS8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, D
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: 2.3 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.426α = 90.00
b = 115.257β = 102.29
c = 73.517γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-07-28 
  • Released Date: 2016-08-03 
  • Deposition Author(s): Cheng, X., Pan, L.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31470749
National Basic Research Program of ChinaChina2013CB836900

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references, Structure summary
  • Version 1.2: 2016-08-17
    Type: Database references