6HOG | pdb_00006hog

Structure of VPS34 LIR motif bound to GABARAP

• PDB DOI: https://doi.org/10.2210/pdb6HOG/pdb

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


• Deposited: 2018-09-17 Released: 2019-02-27 
• Deposition Author(s): Mouilleron, S., Birgisdottir, A.B., Bhujbal, Z., Wirth, M., Sjottem, E., Evjen, G., Zhang, W., Lee, R., O'Reilly, N., Tooze, S., Lamark, T., Johansen, T.
• Funding Organization(s): Research Council of Norway

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 
  0.181 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs.

Birgisdottir, A.B., Mouilleron, S., Bhujabal, Z., Wirth, M., Sjottem, E., Evjen, G., Zhang, W., Lee, R., O'Reilly, N., Tooze, S.A., Lamark, T., Johansen, T.

(2019) Autophagy 15: 1333-1355

• PubMed: 30767700 
• DOI: https://doi.org/10.1080/15548627.2019.1581009
• Primary Citation Related Structures: 
  6HOG, 6HOH, 6HOI, 6HOJ, 6HOK, 6HOL


• PubMed Abstract: 
  

  Autophagosome formation depends on a carefully orchestrated interplay between membrane-associated protein complexes. Initiation of macroautophagy/autophagy is mediated by the ULK1 (unc-51 like autophagy activating kinase 1) protein kinase complex and the autophagy-specific class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1). The latter contains PIK3C3/VPS34, PIK3R4/VPS15, BECN1/Beclin 1 and ATG14 and phosphorylates phosphatidylinositol to generate phosphatidylinositol 3-phosphate (PtdIns3P). Here, we show that PIK3C3, BECN1 and ATG14 contain functional LIR motifs and interact with the Atg8-family proteins with a preference for GABARAP and GABARAPL1. High resolution crystal structures of the functional LIR motifs of these core components of PtdIns3K-C1were obtained. Variation in hydrophobic pocket 2 (HP2) may explain the specificity for the GABARAP family. Mutation of the LIR motif in ATG14 did not prevent formation of the PtdIns3K-C1 complex, but blocked colocalization with MAP1LC3B/LC3B and impaired mitophagy. The ULK-mediated phosphorylation of S29 in ATG14 was strongly dependent on a functional LIR motif in ATG14. GABARAP-preferring LIR motifs in PIK3C3, BECN1 and ATG14 may, via coincidence detection, contribute to scaffolding of PtdIns3K-C1 on membranes for efficient autophagosome formation. Abbreviations: ATG: autophagy-related; BafA1: bafilomycin A ₁ ; GABARAP: GABA type A receptor-associated protein; GABARAPL1: GABA type A receptor associated protein like 1; GFP: enhanced green fluorescent protein; KO: knockout; LDS: LIR docking site; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PIK3C3: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4: phosphoinositide-3-kinase regulatory subunit 4; PtdIns3K: phosphatidylinositol 3-kinase; PtdIns3P: phosphatidylinositol-3-phosphate; SQSTM1/p62: sequestosome 1; VPS: Vacuolar protein sorting; ULK: unc-51 like autophagy activating kinase.

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Organizational Affiliation: 
• a Molecular Cancer Research Group, Department of Medical Biology , University of Tromsø -The Arctic University of Norway , Tromsø , Norway.
b Structural Biology , The Francis Crick Institute , London , UK.
c Molecular Cell Biology of Autophagy Laboratory , The Francis Crick Institute , London , UK.
d Peptide Chemistry Science Technology Platform , The Francis Crick Institute , London , UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 15.69 kDa 
• Atom Count: 1,166 
• Modeled Residue Count: 123 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 3-kinase catalytic subunit type 3,Gamma-aminobutyric acid receptor-associated protein	A	129	Homo sapiens	Mutation(s): 0  Gene Names: PIK3C3, VPS34, GABARAP, FLC3B, HT004 EC: 2.7.1.137
UniProt & NIH Common Fund Data Resources
Find proteins for O95166 (Homo sapiens) Explore O95166  Go to UniProtKB:  O95166
PHAROS:  O95166 GTEx:  ENSG00000170296
Find proteins for Q8NEB9 (Homo sapiens) Explore Q8NEB9  Go to UniProtKB:  Q8NEB9
PHAROS:  Q8NEB9 GTEx:  ENSG00000078142
UniProt Groups	O95166Q8NEB9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free:  0.181 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.1	α = 90
b = 92.1	β = 90
c = 41.23	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Mouilleron, S., Birgisdottir, A.B., Bhujbal, Z., Wirth, M., Sjottem, E., Evjen, G., Zhang, W., Lee, R., O'Reilly, N., Tooze, S., Lamark, T., Johansen, T.

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Funding Organization	Location	Grant Number
Research Council of Norway	Norway	214448
Research Council of Norway	Norway	249884

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-03-13
  Changes: Data collection, Database references
• Version 1.2: 2019-07-10
  Changes: Data collection, Database references
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description