3WIM | pdb_00003wim

GABARAP-LIR peptide complex

• PDB DOI: https://doi.org/10.2210/pdb3WIM/pdb

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


• Deposited: 2013-09-19 Released: 2014-03-12 
• Deposition Author(s): Lystad, A., Ichimura, Y., Takagi, K., Yang, Y., Pankiv, S., Mizushima, T., Komatsu, M., Simonsen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

GABARAP-LIR peptide complex

Lystad, A., Ichimura, Y., Takagi, K., Yang, Y., Pankiv, S., Mizushima, T., Komatsu, M., Simonsen, A.

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)

Macromolecule Content 

• Total Structure Weight: 15.56 kDa 
• Atom Count: 1,099 
• Modeled Residue Count: 129 
• Deposited Residue Count: 131 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor-associated protein	A	117	Homo sapiens	Mutation(s): 0  Gene Names: GABARAP, FLC3B, HT004
UniProt & NIH Common Fund Data Resources
Find proteins for O95166 (Homo sapiens) Explore O95166  Go to UniProtKB:  O95166
PHAROS:  O95166 GTEx:  ENSG00000170296

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat and FYVE domain-containing protein 3	B	14	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZQ1 (Homo sapiens) Explore Q8IZQ1  Go to UniProtKB:  Q8IZQ1
PHAROS:  Q8IZQ1 GTEx:  ENSG00000163625

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.491	α = 90
b = 53.491	β = 90
c = 83.193	γ = 120

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Lystad, A., Ichimura, Y., Takagi, K., Yang, Y., Pankiv, S., Mizushima, T., Komatsu, M., Simonsen, A.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description