7YO9 | pdb_00007yo9

Crystal structure of fusion protein of human TP53INP2 LIR and human GABARAP

• PDB DOI: https://doi.org/10.2210/pdb7YO9/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): 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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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.

---

Organizational Affiliation: 

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

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 15.61 kDa 
• Atom Count: 1,169 
• Modelled Residue Count: 131 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor protein p53-inducible nuclear protein 2,Gamma-aminobutyric acid receptor-associated protein	A	131	Homo sapiens	Mutation(s): 2  Gene Names: TP53INP2, C20orf110, DOR, PINH, GABARAP, FLC3B, HT004
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXH6 (Homo sapiens) Explore Q8IXH6  Go to UniProtKB:  Q8IXH6
PHAROS:  Q8IXH6 GTEx:  ENSG00000078804
Find proteins for O95166 (Homo sapiens) Explore O95166  Go to UniProtKB:  O95166
PHAROS:  O95166 GTEx:  ENSG00000170296
UniProt Groups	Q8IXH6O95166

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
IPA (Subject of Investigation/LOI)	B [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.216 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.39	α = 90
b = 46.39	β = 90
c = 75.4	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

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

---

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