7YO8

Crystal structure of fission yeast Hfl1 LIR fused to human GABARAPL2

• PDB DOI: https://doi.org/10.2210/pdb7YO8/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Schizosaccharomyces pombe, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-08-01 Released: 2022-11-02 
• Deposition Author(s): Yamasaki, A., Noda, N.N.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Literature

Development of new tools to study membrane-anchored mammalian Atg8 proteins.

Park, S.W., Jeon, P., Yamasaki, A., Lee, H.E., Choi, H., Mun, J.Y., Jun, Y.W., Park, J.H., Lee, S.H., Lee, S.K., Lee, Y.K., Song, H.K., Lazarou, M., Cho, D.H., Komatsu, M., Noda, N.N., Jang, D.J., Lee, J.A.

(2023) Autophagy 19: 1424-1443

• PubMed: 36250672 
• DOI: https://doi.org/10.1080/15548627.2022.2132040
• Primary Citation of Related Structures:  
  7YO8, 7YO9


• PubMed Abstract: 
  

  A:C autophagic membrane:cytosol; ALS amyotrophic lateral sclerosis; ATG4 autophagy related 4; Atg8 autophagy related 8; BafA1 bafilomycin A ₁ ; BNIP3L/Nix BCL2 interacting protein 3 like; CALCOCO2/NDP52 calcium binding and coiled-coil domain 2; EBSS Earle's balanced salt solution; GABARAP GABA type A receptor-associated protein; GST glutathione S transferase; HKO hexa knockout; K _d dissociation constant; LIR LC3-interacting region; MAP1LC3/LC3 microtubule associated protein 1 light chain 3; NLS nuclear localization signal/sequence; PE phosphatidylethanolamine; SpHfl1 Schizosaccharomyces pombe organic solute transmembrane transporter; SQSTM1/p62 SQSTM1/p62; TARDBP/TDP-43 TAR DNA binding protein; TKO triple knockout.

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Organizational Affiliation: 

Department of Vector Entomology, College of Ecology and Environment, Kyungpook National University, Sangju, Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 17.25 kDa 
• Atom Count: 1,287 
• Modelled Residue Count: 140 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein 184 homolog C30D11.06c,Gamma-aminobutyric acid receptor-associated protein-like 2	A	147	Schizosaccharomyces pombe, Homo sapiens This entity is chimeric	Mutation(s): 2  Gene Names: SPAC30D11.06c, GABARAPL2, FLC3A, GEF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q09906 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q09906  Go to UniProtKB:  Q09906
Find proteins for P60520 (Homo sapiens) Explore P60520  Go to UniProtKB:  P60520
PHAROS:  P60520 GTEx:  ENSG00000034713
UniProt Groups	P60520Q09906

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.85	α = 90
b = 45.85	β = 90
c = 152.58	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Yamasaki, A., Noda, N.N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18H03989
Japan Society for the Promotion of Science (JSPS)	Japan	19H05707
Japan Society for the Promotion of Science (JSPS)	Japan	17K18339
Japan Science and Technology	Japan	JPMJCR20E3

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description