8BSU

Crystal structure of the kainate receptor GluK3-H523A ligand binding domain in complex with kainate and the positive allosteric modulator BPAM344 at 2.9A resolution

PDB DOI: https://doi.org/10.2210/pdb8BSU/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: 2.90 ?
R-Value Free: 0.234
R-Value Work: 0.207
R-Value Observed: 0.208

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: 240.08 kDa
Atom Count: 16,506
Modelled Residue Count: 2,000
Deposited Residue Count: 2,064
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, E A, B, C, D, E, F, G, H	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
2J9 (Subject of Investigation/LOI) Query on 2J9 Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain I [auth A] SDF format, chain NB [auth F] SDF format, chain OA [auth D] SDF format, chain T [auth B] SDF format, chain WA [auth E] SDF format, chain WB [auth G] SDF format, chain XA [auth E] MOL2 format, chain EA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain NB [auth F] MOL2 format, chain OA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain WB [auth G] MOL2 format, chain XA [auth E] mmCIF format, chain EA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain NB [auth F] mmCIF format, chain OA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain WB [auth G] mmCIF format, chain XA [auth E]	EA [auth C] I [auth A] NB [auth F] OA [auth D] T [auth B] EA [auth C], I [auth A], NB [auth F], OA [auth D], T [auth B], WA [auth E], WB [auth G], XA [auth E]	4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide C₁₀ H₁₁ F N₂ O₂ S FLTMTBPCYAZIKM-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain I [auth A] Focus chain NB [auth F] Focus chain OA [auth D] Focus chain T [auth B] Focus chain WA [auth E] Focus chain WB [auth G] Focus chain XA [auth E] Interactions & Density Focus chain EA [auth C] Focus chain I [auth A] Focus chain NB [auth F] Focus chain OA [auth D] Focus chain T [auth B] Focus chain WA [auth E] Focus chain WB [auth G] Focus chain XA [auth E]
KAI (Subject of Investigation/LOI) Query on KAI Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DC [auth G] SDF format, chain LC [auth H] SDF format, chain MB [auth E] SDF format, chain NA [auth C] SDF format, chain R [auth A] SDF format, chain UB [auth F] SDF format, chain VA [auth D] MOL2 format, chain CA [auth B] MOL2 format, chain DC [auth G] MOL2 format, chain LC [auth H] MOL2 format, chain MB [auth E] MOL2 format, chain NA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain UB [auth F] MOL2 format, chain VA [auth D] mmCIF format, chain CA [auth B] mmCIF format, chain DC [auth G] mmCIF format, chain LC [auth H] mmCIF format, chain MB [auth E] mmCIF format, chain NA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain UB [auth F] mmCIF format, chain VA [auth D]	CA [auth B] DC [auth G] LC [auth H] MB [auth E] NA [auth C] CA [auth B], DC [auth G], LC [auth H], MB [auth E], NA [auth C], R [auth A], UB [auth F], VA [auth D]	3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE C₁₀ H₁₅ N O₄ VLSMHEGGTFMBBZ-OOZYFLPDSA-N		Interactions Focus chain CA [auth B] Focus chain DC [auth G] Focus chain LC [auth H] Focus chain MB [auth E] Focus chain NA [auth C] Focus chain R [auth A] Focus chain UB [auth F] Focus chain VA [auth D] Interactions & Density Focus chain CA [auth B] Focus chain DC [auth G] Focus chain LC [auth H] Focus chain MB [auth E] Focus chain NA [auth C] Focus chain R [auth A] Focus chain UB [auth F] Focus chain VA [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CC [auth G] SDF format, chain KC [auth H] SDF format, chain LB [auth E] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain TA [auth D] SDF format, chain UA [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain CC [auth G] MOL2 format, chain KC [auth H] MOL2 format, chain LB [auth E] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain CC [auth G] mmCIF format, chain KC [auth H] mmCIF format, chain LB [auth E] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D]	BA [auth B] CC [auth G] KC [auth H] LB [auth E] P [auth A] BA [auth B], CC [auth G], KC [auth H], LB [auth E], P [auth A], Q [auth A], TA [auth D], UA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth B] Focus chain CC [auth G] Focus chain KC [auth H] Focus chain LB [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Interactions & Density Focus chain BA [auth B] Focus chain CC [auth G] Focus chain KC [auth H] Focus chain LB [auth E] Focus chain P [auth A] Focus chain Q [auth A] Focus chain TA [auth D] Focus chain UA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EB [auth E] SDF format, chain FB [auth E] SDF format, chain GB [auth E] SDF format, chain GC [auth H] SDF format, chain HA [auth C] SDF format, chain HB [auth E] SDF format, chain IA [auth C] SDF format, chain IB [auth E] SDF format, chain JB [auth E] SDF format, chain L [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain W [auth B] MOL2 format, chain EB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain GB [auth E] MOL2 format, chain GC [auth H] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain JB [auth E] MOL2 format, chain L [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain W [auth B] mmCIF format, chain EB [auth E] mmCIF format, chain FB [auth E] mmCIF format, chain GB [auth E] mmCIF format, chain GC [auth H] mmCIF format, chain HA [auth C] mmCIF format, chain HB [auth E] mmCIF format, chain IA [auth C] mmCIF format, chain IB [auth E] mmCIF format, chain JB [auth E] mmCIF format, chain L [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain W [auth B]	EB [auth E] FB [auth E] GB [auth E] GC [auth H] HA [auth C] EB [auth E], FB [auth E], GB [auth E], GC [auth H], HA [auth C], HB [auth E], IA [auth C], IB [auth E], JB [auth E], L [auth A], RA [auth D], SA [auth D], W [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain GC [auth H] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain L [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B] Interactions & Density Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GB [auth E] Focus chain GC [auth H] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain JB [auth E] Focus chain L [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain W [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain CB [auth E] SDF format, chain DB [auth E] SDF format, chain EC [auth H] SDF format, chain FA [auth C] SDF format, chain FC [auth H] SDF format, chain GA [auth C] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain OB [auth F] SDF format, chain PA [auth D] SDF format, chain PB [auth F] SDF format, chain QA [auth D] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain XB [auth G] SDF format, chain YA [auth E] SDF format, chain YB [auth G] SDF format, chain ZA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EC [auth H] MOL2 format, chain FA [auth C] MOL2 format, chain FC [auth H] MOL2 format, chain GA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain PA [auth D] MOL2 format, chain PB [auth F] MOL2 format, chain QA [auth D] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain XB [auth G] MOL2 format, chain YA [auth E] MOL2 format, chain YB [auth G] MOL2 format, chain ZA [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain CB [auth E] mmCIF format, chain DB [auth E] mmCIF format, chain EC [auth H] mmCIF format, chain FA [auth C] mmCIF format, chain FC [auth H] mmCIF format, chain GA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain OB [auth F] mmCIF format, chain PA [auth D] mmCIF format, chain PB [auth F] mmCIF format, chain QA [auth D] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain XB [auth G] mmCIF format, chain YA [auth E] mmCIF format, chain YB [auth G] mmCIF format, chain ZA [auth E]	AB [auth E] BB [auth E] CB [auth E] DB [auth E] EC [auth H] AB [auth E], BB [auth E], CB [auth E], DB [auth E], EC [auth H], FA [auth C], FC [auth H], GA [auth C], J [auth A], K [auth A], OB [auth F], PA [auth D], PB [auth F], QA [auth D], U [auth B], V [auth B], XB [auth G], YA [auth E], YB [auth G], ZA [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EC [auth H] Focus chain FA [auth C] Focus chain FC [auth H] Focus chain GA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain OB [auth F] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain QA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain XB [auth G] Focus chain YA [auth E] Focus chain YB [auth G] Focus chain ZA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EC [auth H] Focus chain FA [auth C] Focus chain FC [auth H] Focus chain GA [auth C] Focus chain J [auth A] Focus chain K [auth A] Focus chain OB [auth F] Focus chain PA [auth D] Focus chain PB [auth F] Focus chain QA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain XB [auth G] Focus chain YA [auth E] Focus chain YB [auth G] Focus chain ZA [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain S [auth A] SDF format, chain VB [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain VB [auth F] mmCIF format, chain DA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain VB [auth F]	DA [auth B], S [auth A], VB [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth B] Focus chain S [auth A] Focus chain VB [auth F] Interactions & Density Focus chain DA [auth B] Focus chain S [auth A] Focus chain VB [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AC [auth G] SDF format, chain BC [auth G] SDF format, chain HC [auth H] SDF format, chain IC [auth H] SDF format, chain JA [auth C] SDF format, chain JC [auth H] SDF format, chain KA [auth C] SDF format, chain KB [auth E] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain QB [auth F] SDF format, chain RB [auth F] SDF format, chain SB [auth F] SDF format, chain TB [auth F] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain ZB [auth G] MOL2 format, chain AA [auth B] MOL2 format, chain AC [auth G] MOL2 format, chain BC [auth G] MOL2 format, chain HC [auth H] MOL2 format, chain IC [auth H] MOL2 format, chain JA [auth C] MOL2 format, chain JC [auth H] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth E] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain QB [auth F] MOL2 format, chain RB [auth F] MOL2 format, chain SB [auth F] MOL2 format, chain TB [auth F] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZB [auth G] mmCIF format, chain AA [auth B] mmCIF format, chain AC [auth G] mmCIF format, chain BC [auth G] mmCIF format, chain HC [auth H] mmCIF format, chain IC [auth H] mmCIF format, chain JA [auth C] mmCIF format, chain JC [auth H] mmCIF format, chain KA [auth C] mmCIF format, chain KB [auth E] mmCIF format, chain LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain QB [auth F] mmCIF format, chain RB [auth F] mmCIF format, chain SB [auth F] mmCIF format, chain TB [auth F] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain ZB [auth G]	AA [auth B] AC [auth G] BC [auth G] HC [auth H] IC [auth H] AA [auth B], AC [auth G], BC [auth G], HC [auth H], IC [auth H], JA [auth C], JC [auth H], KA [auth C], KB [auth E], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], QB [auth F], RB [auth F], SB [auth F], TB [auth F], X [auth B], Y [auth B], Z [auth B], ZB [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AC [auth G] Focus chain BC [auth G] Focus chain HC [auth H] Focus chain IC [auth H] Focus chain JA [auth C] Focus chain JC [auth H] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain TB [auth F] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth G] Interactions & Density Focus chain AA [auth B] Focus chain AC [auth G] Focus chain BC [auth G] Focus chain HC [auth H] Focus chain IC [auth H] Focus chain JA [auth C] Focus chain JC [auth H] Focus chain KA [auth C] Focus chain KB [auth E] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain QB [auth F] Focus chain RB [auth F] Focus chain SB [auth F] Focus chain TB [auth F] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth G]