4KFV | pdb_00004kfv

Structural insight into Golgi membrane stacking by GRASP65 and GRASP55

• PDB DOI: https://doi.org/10.2210/pdb4KFV/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-04-28 Released: 2013-08-21 
• Deposition Author(s): Liu, X., Hu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.283 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Structural insight into Golgi membrane stacking by GRASP65 and GRASP55 proteins

Feng, Y., Yu, W., Li, X., Lin, S., Zhou, Y., Hu, J., Liu, X.

(2013) J Biological Chem 288: 28418-28427

• PubMed: 23940043 
• DOI: https://doi.org/10.1074/jbc.M113.478024
• Primary Citation Related Structures: 
  4KFV, 4KFW


• PubMed Abstract: 
  

  The stacking of Golgi cisternae involves GRASP65 and GRASP55. The oligomerization of the N-terminal GRASP domain of these proteins, which consists of two tandem PDZ domains, is required to tether the Golgi membranes. However, the molecular basis for GRASP assembly is unclear. Here, we determined the crystal structures of the GRASP domain of GRASP65 and GRASP55. The structures reveal similar homotypic interactions: the GRASP domain forms a dimer in which the peptide-binding pockets of the two neighboring PDZ2 domains face each other, and the dimers are further connected by the C-terminal tail of one GRASP domain inserting into the binding pocket of the PDZ1 domain in another dimer. Biochemical analysis suggests that both types of contacts are relatively weak but are needed in combination for GRASP-mediated Golgi stacking. Our results unveil a novel mode of membrane tethering by GRASP proteins and provide insight into the mechanism of Golgi stacking.

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Organizational Affiliation: 
• From the Department of Biochemistry and Molecular Biology, College of Life Sciences, and State Key Laboratory of Medicinal Chemical Biology and.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 23.15 kDa 
• Atom Count: 1,648 
• Modeled Residue Count: 199 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Golgi reassembly-stacking protein 1	A	210	Rattus norvegicus	Mutation(s): 0  Gene Names: Gorasp1, GRASP 65, rCG_25352
UniProt
Find proteins for O35254 (Rattus norvegicus) Explore O35254  Go to UniProtKB:  O35254

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.283 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.989	α = 90
b = 104.287	β = 90
c = 37.932	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Liu, X., Hu, J.

Revision History  

• Version 1.0: 2013-08-21
  Type: Initial release
  
• Version 1.1: 2014-01-22
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations