3DOW | pdb_00003dow

Complex structure of GABA type A receptor associated protein and its binding epitope on calreticulin

• PDB DOI: https://doi.org/10.2210/pdb3DOW/pdb

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


• Deposited: 2008-07-07 Released: 2009-02-24 
• Deposition Author(s): Thielmann, Y., Weiergraeber, O.H., Willbold, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.270 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Structural framework of the GABARAP-calreticulin interface - implications for substrate binding to endoplasmic reticulum chaperones.

Thielmann, Y., Weiergraber, O.H., Mohrluder, J., Willbold, D.

(2009) FEBS J 276: 1140-1152

• PubMed: 19154346 
• DOI: https://doi.org/10.1111/j.1742-4658.2008.06857.x
• Primary Citation Related Structures: 
  3DOW


• PubMed Abstract: 
  

  The 4-aminobutyrate type A receptor-associated protein (GABARAP) is a versatile adaptor protein that plays an important role in intracellular vesicle trafficking, particularly in neuronal cells. We have investigated the structural determinants underlying the interaction of GABARAP with calreticulin using spectroscopic and crystallographic techniques. Specifically, we present the crystal structure of GABARAP in complex with its major binding epitope on the chaperone. Molecular modeling of a complex containing full-length calreticulin suggests a novel mode of substrate interaction, which may have functional implications for the calreticulin/calnexin family in general.

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Organizational Affiliation: 
• Institut für Neurowissenschaften und Biophysik, Molekulare Biophysik, Forschungszentrum Jülich, Germany.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.48 kDa 
• Atom Count: 1,066 
• Modeled Residue Count: 127 
• 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	119	Homo sapiens	Mutation(s): 0  Gene Names: GABARAP, FLC3B
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
CRT peptide	B	12	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P27797 (Homo sapiens) Explore P27797  Go to UniProtKB:  P27797
PHAROS:  P27797 GTEx:  ENSG00000179218

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.270 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.043	α = 90
b = 97.043	β = 90
c = 97.043	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-24 
Deposition Author(s): Thielmann, Y., Weiergraeber, O.H., Willbold, D.

Revision History  

• Version 1.0: 2009-02-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary