9N4S | pdb_00009n4s

Composite map for GluK2-1xNeto2 in the open state, in complex with the positive allosteric modulator BPAM344 and agonist kainate


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Activation of kainate receptor GluK2-Neto2 complex.

Gangwar, S.P.Yelshanskaya, M.V.Yen, L.Y.Newton, T.P.Sobolevsky, A.I.

(2025) Nat Struct Mol Biol 32: 2176-2184

  • DOI: https://doi.org/10.1038/s41594-025-01656-9
  • Primary Citation of Related Structures:  
    9N4L, 9N4M, 9N4N, 9N4O, 9N4P, 9N4Q, 9N4R, 9N4S, 9N4T

  • PubMed Abstract: 

    Kainate receptors (KARs) are tetrameric, ligand-gated ion channels of the ionotropic glutamate receptor family that mediate excitatory neurotransmission and modulate neuronal circuits and synaptic plasticity during development of the central nervous system. KARs are implicated in psychiatric and neurological diseases and represent a target of therapeutic intervention. Native KARs form complexes with neuropilin and tolloid-like auxiliary subunits (Neto1 and Neto2), which modulate their function, trafficking and synaptic localization. Here we present structures of rat GluK2 KAR in the apo closed state and in the open states activated by agonist kainate and positive allosteric modulator BPAM344, solved in the presence and absence of Neto2 using time-resolved cryo-electron microscopy. While the binding of Neto2 does not change the behavior of individual or dimeric ligand-binding domains (LBDs) or the ion channel, it prevents tightening of the interface between two LBD dimers during activation and slows the kinetics of deactivation. Our structures illuminate the mechanism of KAR activation and its modulation by Neto2.


  • 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
908Rattus 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: 7Go to GlyGen: P42260-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neuropilin and tolloid-like protein 2525Rattus norvegicusMutation(s): 0 
Gene Names: Neto2Btcl2
Membrane Entity: Yes 
UniProt
Find proteins for C6K2K4 (Rattus norvegicus)
Explore C6K2K4 
Go to UniProtKB:  C6K2K4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6K2K4
Glycosylation
Glycosylation Sites: 1Go to GlyGen: C6K2K4-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
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
F, I, K, N
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, M
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J, L, O
4N-Glycosylation
Glycosylation Resources
GlyTouCan:  G31886NL
GlyCosmos:  G31886NL
GlyGen:  G31886NL
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
AB [auth D]
BB [auth D]
DA [auth B]
EA [auth B]
FA [auth B]
AB [auth D],
BB [auth D],
DA [auth B],
EA [auth B],
FA [auth B],
LA [auth B],
NA [auth C],
OA [auth C],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
VA [auth D],
WA [auth D],
YA [auth D],
Z [auth A],
ZA [auth D]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
2J9 (Subject of Investigation/LOI)
Query on 2J9

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth B],
KA [auth B],
UA [auth D]
4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide
C10 H11 F N2 O2 S
FLTMTBPCYAZIKM-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CB [auth D]
DB [auth D]
EB [auth D]
FB [auth D]
GA [auth B]
CB [auth D],
DB [auth D],
EB [auth D],
FB [auth D],
GA [auth B],
GB [auth E],
HA [auth B],
IA [auth B],
JA [auth B],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
KAI (Subject of Investigation/LOI)
Query on KAI

Download Ideal Coordinates CCD File 
CA [auth B],
MA [auth C],
P [auth A],
XA [auth D]
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
C10 H15 N O4
VLSMHEGGTFMBBZ-OOZYFLPDSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.11.1_2575:
RECONSTRUCTIONcryoSPARC

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
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR21 NS139087

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references