Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.22 kDa 
• Atom Count: 1141 
• Modelled Residue Count: 137 
• Deposited Residue Count: 137 
• Unique protein chains: 2

2N9X

LC3 FUNDC1 complex structure

• PDB DOI: 10.2210/pdb2N9X/pdb
• BMRB: 25919

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


• Deposited: 2015-12-14 Released: 2016-12-14 
• Deposition Author(s): Xia, B., Kuang, Y.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structural basis for the phosphorylation of FUNDC1 LIR as a molecular switch of mitophagy.

Kuang, Y., Ma, K., Zhou, C., Ding, P., Zhu, Y., Chen, Q., Xia, B.

(2016) Autophagy 12: 2363-2373

• PubMed: 27653272 
• DOI: 10.1080/15548627.2016.1238552
• Primary Citation of Related Structures:  
  2N9X


• PubMed Abstract: 
  

Mitophagy is a fundamental process that determines mitochondrial quality and homeostasis. Several mitophagy receptors, including the newly identified FUNDC1, mediate selective removal of damaged or superfluous mitochondria through their specific interaction with LC3. However, the precise mechanism by which this interaction is regulated to initiate mitophagy is not understood. Here, we report the solution structure of LC3 in complex with a peptide containing the FUNDC1 LC3-interacting region (LIR) motif. The structure reveals a noncanonical LC3-LIR binding conformation, in which the third LIR residue (Val20) is also inserted into the hydrophobic pocket of LC3, together with the conserved residues Tyr18 and Leu21. This enables Tyr18 to be positioned near Asp19 of LC3, and thus phosphorylation of Tyr18 significantly weakens the binding affinity due to electrostatic repulsion. Functional analysis revealed that mitochondrial targeting of the LIR-containing cytosolic portion of FUNDC1 is necessary and sufficient to initiate mitophagy when Tyr18 is unphosphorylated, even in the absence of mitochondrial fragmentation. Thus, we demonstrated that phosphorylation of Tyr18 of FUNDC1 serves as a molecular switch for mitophagy. This may represent a novel target for therapeutic intervention.

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Organizational Affiliation: 

a Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University , Beijing , China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microtubule-associated proteins 1A/1B light chain 3B	A	120	Homo sapiens	Mutation(s): 0  Gene Names: MAP1LC3B, MAP1ALC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZQ8 (Homo sapiens) Explore Q9GZQ8  Go to UniProtKB:  Q9GZQ8
PHAROS:  Q9GZQ8 GTEx:  ENSG00000140941

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FUN14 domain-containing protein 1	B	17	Homo sapiens	Mutation(s): 0  Gene Names: FUNDC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVP5 (Homo sapiens) Explore Q8IVP5  Go to UniProtKB:  Q8IVP5
PHAROS:  Q8IVP5 GTEx:  ENSG00000069509

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2N9X Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-12-14 
• Released Date: 2016-12-14 
Deposition Author(s): Xia, B., Kuang, Y.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references