4H8I | pdb_00004h8i

Structure of GluK2-LBD in complex with GluAzo

• PDB DOI: https://doi.org/10.2210/pdb4H8I/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-22 Released: 2013-09-25 
• Deposition Author(s): Reiter, A., Skerra, A., Trauner, D., Schiefner, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

A photoswitchable neurotransmitter analogue bound to its receptor.

Reiter, A., Skerra, A., Trauner, D., Schiefner, A.

(2013) Biochemistry 52: 8972-8974

• PubMed: 24295282 
• DOI: https://doi.org/10.1021/bi4014402
• Primary Citation of Related Structures:  
  4H8I


• PubMed Abstract: 
  

  Incorporation of the azobenzene derivative gluazo, a synthetic photochromic ligand, into a kainate receptor allows for the optical control of neuronal activity. The crystal structure of gluazo bound to a dimeric GluK2 ligand-binding domain reveals one monomer in a closed conformation, occupied by gluazo, and the other in an open conformation, with a bound buffer molecule. The glutamate group of gluazo interacts like the natural glutamate ligand, while its trans-azobenzene moiety protrudes into a tunnel. This elongated cavity presumably cannot accommodate a cis-azobenzene, which explains the reversible activation of the receptor upon photoisomerization.

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Organizational Affiliation: 

Munich Center for Integrated Protein Science (CIPS-M).

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 59.44 kDa 
• Atom Count: 4,645 
• Modelled Residue Count: 512 
• Deposited Residue Count: 518 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor, ionotropic kainate 2	A, B	259	Rattus norvegicus	Mutation(s): 0  Gene Names: Glur6, Grik2
UniProt
Find proteins for P42260 (Rattus norvegicus) Explore P42260  Go to UniProtKB:  P42260

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
11W	C [auth A]	(4R)-4-[(2E)-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-en-1-yl]-L-glutamic acid C20 H21 N3 O4 MUSRDKYERZDIAD-MTDKYJNHSA-N
MES	F [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.609	α = 90
b = 102.609	β = 90
c = 282.513	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Reiter, A., Skerra, A., Trauner, D., Schiefner, A.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-27
  Changes: Structure summary