6YOO | pdb_00006yoo

Structure of SAMM50 LIR bound to GABARAPL1

• PDB DOI: https://doi.org/10.2210/pdb6YOO/pdb

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


• Deposited: 2020-04-14 Released: 2021-04-28 
• Deposition Author(s): Mouilleron, S., Wenxin, Z., Johansen, T., Tooze, S., Abudu, Y.P., Lamark, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.134 (Depositor) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Structure of SAMM50 LIR bound to GABARAPL1

Mouilleron, S., Wenxin, Z., Johansen, T., Tooze, S., Abudu, Y.P., Lamark, T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 16.27 kDa 
• Atom Count: 1,361 
• Modeled Residue Count: 128 
• Deposited Residue Count: 135 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor-associated protein-like 1	A	123	Homo sapiens	Mutation(s): 0  Gene Names: GABARAPL1, GEC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0R8 (Homo sapiens) Explore Q9H0R8  Go to UniProtKB:  Q9H0R8
PHAROS:  Q9H0R8 GTEx:  ENSG00000139112

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting and assembly machinery component 50 homolog	B	12	Homo sapiens	Mutation(s): 0  Gene Names: SAMM50, SAM50, CGI-51, TRG3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y512 (Homo sapiens) Explore Q9Y512  Go to UniProtKB:  Q9Y512
PHAROS:  Q9Y512 GTEx:  ENSG00000100347

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.134 (Depositor) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.98	α = 90
b = 54.04	β = 90
c = 62.07	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Mouilleron, S., Wenxin, Z., Johansen, T., Tooze, S., Abudu, Y.P., Lamark, T.

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description