3RLE | pdb_00003rle

Crystal Structure of GRASP55 GRASP domain (residues 7-208)

• PDB DOI: https://doi.org/10.2210/pdb3RLE/pdb

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


• Deposited: 2011-04-19 Released: 2011-05-04 
• Deposition Author(s): Truschel, S.T., Sengupta, D., Foote, A., Heroux, A., Macbeth, M.R., Linstedt, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.222 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Structure of the Membrane-tethering GRASP Domain Reveals a Unique PDZ Ligand Interaction That Mediates Golgi Biogenesis.

Truschel, S.T., Sengupta, D., Foote, A., Heroux, A., Macbeth, M.R., Linstedt, A.D.

(2011) J Biological Chem 286: 20125-20129

• PubMed: 21515684 
• DOI: https://doi.org/10.1074/jbc.C111.245324
• Primary Citation Related Structures: 
  3RLE


• PubMed Abstract: 
  

  Biogenesis of the ribbon-like membrane network of the mammalian Golgi requires membrane tethering by the conserved GRASP domain in GRASP65 and GRASP55, yet the tethering mechanism is not fully understood. Here, we report the crystal structure of the GRASP55 GRASP domain, which revealed an unusual arrangement of two tandem PDZ folds that more closely resemble prokaryotic PDZ domains. Biochemical and functional data indicated that the interaction between the ligand-binding pocket of PDZ1 and an internal ligand on PDZ2 mediates the GRASP self-interaction, and structural analyses suggest that this occurs via a unique mode of internal PDZ ligand recognition. Our data uncover the structural basis for ligand specificity and provide insight into the mechanism of GRASP-dependent membrane tethering of analogous Golgi cisternae.

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Organizational Affiliation: 
• Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA.

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: 22.99 kDa 
• Atom Count: 1,842 
• Modeled Residue Count: 202 
• Deposited Residue Count: 209 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Golgi reassembly-stacking protein 2	A	209	Homo sapiens	Mutation(s): 0  Gene Names: GORASP2, GOLPH6
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H8Y8 (Homo sapiens) Explore Q9H8Y8  Go to UniProtKB:  Q9H8Y8
PHAROS:  Q9H8Y8 GTEx:  ENSG00000115806

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.222 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.04	α = 90
b = 88.04	β = 90
c = 61.195	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Truschel, S.T., Sengupta, D., Foote, A., Heroux, A., Macbeth, M.R., Linstedt, A.D.

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary