8BST

Crystal structure of the kainate receptor GluK3-H523A ligand binding domain in complex with kainate at 2.7A resolution

PDB DOI: https://doi.org/10.2210/pdb8BST/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-11-26 Released: 2023-12-13
Deposition Author(s): Venskutonyte, R., Frydenvang, K., Kastrup, J.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.238
R-Value Work: 0.204
R-Value Observed: 0.205

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Small-molecule positive allosteric modulation of homomeric kainate receptors GluK1-3: development of screening assays and insight into GluK3 structure.

Bay, Y., Venskutonyte, R., Frantsen, S.M., Thorsen, T.S., Musgaard, M., Frydenvang, K., Francotte, P., Pirotte, B., Biggin, P.C., Kristensen, A.S., Boesen, T., Pickering, D.S., Gajhede, M., Kastrup, J.S.

(2024) FEBS J 291: 1506-1529

PubMed: 38145505 Search on PubMed
DOI: https://doi.org/10.1111/febs.17046
Primary Citation of Related Structures:
8BST, 8BSU

PubMed Abstract:
The kainate receptors GluK1-3 (glutamate receptor ionotropic, kainate receptors 1-3) belong to the family of ionotropic glutamate receptors and are essential for fast excitatory neurotransmission in the brain, and are associated with neurological and psychiatric diseases. How these receptors can be modulated by small-molecule agents is not well understood, especially for GluK3. We show that the positive allosteric modulator BPAM344 can be used to establish robust calcium-sensitive fluorescence-based assays to test agonists, antagonists, and positive allosteric modulators of GluK1-3. The half-maximal effective concentration (EC ₅₀) of BPAM344 for potentiating the response of 100 μm kainate was determined to be 26.3 μm for GluK1, 75.4 μm for GluK2, and 639 μm for GluK3. Domoate was found to be a potent agonist for GluK1 and GluK2, with an EC ₅₀ of 0.77 and 1.33 μm, respectively, upon co-application of 150 μm BPAM344. At GluK3, domoate acts as a very weak agonist or antagonist with a half-maximal inhibitory concentration (IC ₅₀) of 14.5 μm, in presence of 500 μm BPAM344 and 100 μm kainate for competition binding. Using H523A-mutated GluK3, we determined the first dimeric structure of the ligand-binding domain by X-ray crystallography, allowing location of BPAM344, as well as zinc-, sodium-, and chloride-ion binding sites at the dimer interface. Molecular dynamics simulations support the stability of the ion sites as well as the involvement of Asp761, Asp790, and Glu797 in the binding of zinc ions. Using electron microscopy, we show that, in presence of glutamate and BPAM344, full-length GluK3 adopts a dimer-of-dimers arrangement.

Organizational Affiliation

Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.

Macromolecule Content

Total Structure Weight: 119.93 kDa
Atom Count: 8,240
Modelled Residue Count: 994
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, kainate 3	A, B, C, D	258	Rattus norvegicus	Mutation(s): 1 Gene Names: Grik3, Glur7
UniProt
Find proteins for P42264 (Rattus norvegicus) Explore P42264 Go to UniProtKB: P42264
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42264
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KAI (Subject of Investigation/LOI) Query on KAI Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain PA [auth C] SDF format, chain R [auth A] SDF format, chain WA [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain WA [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain WA [auth D]	EA [auth B], PA [auth C], R [auth A], WA [auth D]	3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE C₁₀ H₁₅ N O₄ VLSMHEGGTFMBBZ-OOZYFLPDSA-N		Interactions Focus chain EA [auth B] Focus chain PA [auth C] Focus chain R [auth A] Focus chain WA [auth D] Interactions & Density Focus chain EA [auth B] Focus chain PA [auth C] Focus chain R [auth A] Focus chain WA [auth D]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain VA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain VA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain VA [auth D]	CA [auth B] DA [auth B] M [auth A] MA [auth C] N [auth A] CA [auth B], DA [auth B], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], VA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain VA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain VA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain S [auth A] SDF format, chain XA [auth D] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain XA [auth D] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain XA [auth D]	FA [auth B], GA [auth B], HA [auth B], S [auth A], XA [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain S [auth A] Focus chain XA [auth D] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain S [auth A] Focus chain XA [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain SA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain SA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain SA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] JA [auth C] G [auth A], H [auth A], I [auth A], J [auth A], JA [auth C], KA [auth C], SA [auth D], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain SA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain SA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain IA [auth C] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain T [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain T [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain T [auth B]	E [auth A] F [auth A] IA [auth C] QA [auth D] RA [auth D] E [auth A], F [auth A], IA [auth C], QA [auth D], RA [auth D], T [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain IA [auth C] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain T [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain IA [auth C] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain T [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain TA [auth D] SDF format, chain UA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D]	AA [auth B] BA [auth B] K [auth A] L [auth A] LA [auth C] AA [auth B], BA [auth B], K [auth A], L [auth A], LA [auth C], TA [auth D], UA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain TA [auth D] Focus chain UA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth C] Focus chain TA [auth D] Focus chain UA [auth D]