5WRD

Crystal structure of LC3B in complex with FYCO1 LIR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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This is version 1.1 of the entry. See complete history


Literature

The crystal structure of mouse LC3B in complex with the FYCO1 LIR reveals the importance of the flanking region of the LIR motif

Sakurai, S.Tomita, T.Shimizu, T.Ohto, U.

(2017) Acta Crystallogr F Struct Biol Commun 73: 130-137

  • DOI: 10.1107/S2053230X17001911
  • Primary Citation of Related Structures:  
    5WRD

  • PubMed Abstract: 
  • FYVE and coiled-coil domain-containing protein 1 (FYCO1), a multidomain autophagy adaptor protein, mediates microtubule plus-end-directed autophagosome transport by interacting with kinesin motor proteins and with the autophagosomal membrane componen ...

    FYVE and coiled-coil domain-containing protein 1 (FYCO1), a multidomain autophagy adaptor protein, mediates microtubule plus-end-directed autophagosome transport by interacting with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7 and phosphatidylinositol 3-phosphate (PI3P). To establish the structural basis for the recognition of FYCO1 by LC3, the crystal structure of mouse LC3B in complex with the FYCO1 LC3-interacting region (LIR) motif peptide was determined. Structural analysis showed that the flanking sequences N-terminal and C-terminal to the LIR core sequence of FYCO1, as well as the tetrapeptide core sequence, were specifically recognized by LC3B and contributed to the binding. Moreover, comparisons of related structures revealed a conserved mechanism of FYCO1 recognition by different LC3 isoforms among different species.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Microtubule-associated proteins 1A/1B light chain 3BAB125Mus musculusMutation(s): 0 
Gene Names: Map1lc3bMap1alc3Map1lc3
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:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptide from FYVE and coiled-coil domain-containing protein 1CD19Mus musculusMutation(s): 0 
Gene Names: Fyco1
Find proteins for Q8VDC1 (Mus musculus)
Explore Q8VDC1 
Go to UniProtKB:  Q8VDC1
NIH Common Fund Data Resources
IMPC  MGI:107277
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.412α = 90
b = 44.613β = 120.29
c = 63.582γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection