4Z0I | pdb_00004z0i

Crystal structure of a tetramer of GluA2 ligand binding domains bound with glutamate at 1.45 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4Z0I/pdb

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


• Deposited: 2015-03-26 Released: 2016-01-13 
• Deposition Author(s): Baranovic, J., Chebli, M., Salazar, H., Carbone, A.L., Ghisi, V., Faelber, K., Lau, A.Y., Daumke, O., Plested, A.J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the tetrameric wt GluA2 ligand-binding domain bound to glutamate at 1.45 Angstroms resolution

Baranovic, J., Chebli, M., Salazar, H., Carbone, A.L., Ghisi, V., Faelber, K., Lau, A.Y., Daumke, O., Plested, A.J.R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.61 kDa 
• Atom Count: 5,126 
• Modeled Residue Count: 525 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor 2,Glutamate receptor 2	A, B	263	Rattus norvegicus	Mutation(s): 0  Gene Names: Gria2, Glur2
UniProt
Find proteins for P19491 (Rattus norvegicus) Explore P19491  Go to UniProtKB:  P19491

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	G [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GLU	C [auth A], I [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
PEG	H [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.19	α = 90
b = 47.27	β = 93.57
c = 116.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
PHASER	phasing
Coot	model building
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-13 
Deposition Author(s): Baranovic, J., Chebli, M., Salazar, H., Carbone, A.L., Ghisi, V., Faelber, K., Lau, A.Y., Daumke, O., Plested, A.J.R.

Revision History  

• Version 1.0: 2016-01-13
  Type: Initial release
  
• Version 2.0: 2020-03-25
  Changes: Atomic model, Derived calculations
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-11-13
  Changes: Structure summary