9B39

Kainate receptor GluK2 in complex with agonist glutamate with asymmetric ligand-binding domain layer

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Rattus norvegicus
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTMMemProtMD

  • Deposited: 2024-03-18 Released: 2024-05-22 
  • Deposition Author(s): Nadezhdin, K.D., Gangwar, S.P., Sobolevsky, A.I.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Kainate receptor channel opening and gating mechanism.

Gangwar, S.P.Yelshanskaya, M.V.Nadezhdin, K.D.Yen, L.Y.Newton, T.P.Aktolun, M.Kurnikova, M.G.Sobolevsky, A.I.

(2024) Nature 630: 762-768

  • DOI: https://doi.org/10.1038/s41586-024-07475-0
  • Primary Citation of Related Structures:  
    9B33, 9B34, 9B35, 9B36, 9B37, 9B38, 9B39

  • PubMed Abstract: 

    Kainate receptors, a subclass of ionotropic glutamate receptors, are tetrameric ligand-gated ion channels that mediate excitatory neurotransmission 1-4 . Kainate receptors modulate neuronal circuits and synaptic plasticity during the development and function of the central nervous system and are implicated in various neurological and psychiatric diseases, including epilepsy, depression, schizophrenia, anxiety and autism 5-11 . Although structures of kainate receptor domains and subunit assemblies are available 12-18 , the mechanism of kainate receptor gating remains poorly understood. Here we present cryo-electron microscopy structures of the kainate receptor GluK2 in the presence of the agonist glutamate and the positive allosteric modulators lectin concanavalin A and BPAM344. Concanavalin A and BPAM344 inhibit kainate receptor desensitization and prolong activation by acting as a spacer between the amino-terminal and ligand-binding domains and a stabilizer of the ligand-binding domain dimer interface, respectively. Channel opening involves the kinking of all four pore-forming M3 helices. Our structures reveal the molecular basis of kainate receptor gating, which could guide the development of drugs for treatment of neurological disorders.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, kainate 2
A, B, C, D
912Rattus norvegicusMutation(s): 0 
Gene Names: Grik2Glur6
Membrane Entity: Yes 
UniProt
Find proteins for P42260 (Rattus norvegicus)
Explore P42260 
Go to UniProtKB:  P42260
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42260
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P42260-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, J, K, L
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, M, N
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
HA [auth D],
IA [auth D],
JA [auth D],
KA [auth D],
LA [auth D],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
GA [auth D],
O [auth A],
T [auth B],
Z [auth C]
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS107253
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01 AR078814
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA206573

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references
  • Version 1.2: 2024-06-26
    Changes: Data collection, Database references
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary