Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural Basis of Functional Transitions in Mammalian NMDA Receptors.
Journal, issue, pages	Cell, Vol. 182, Issue 2, Page 357-371.e13, Year 2020
Publish date	Jul 23, 2020
Authors	Tsung-Han Chou / Nami Tajima / Annabel Romero-Hernandez / Hiro Furukawa /
PubMed Abstract	Excitatory neurotransmission meditated by glutamate receptors including N-methyl-D-aspartate receptors (NMDARs) is pivotal to brain development and function. NMDARs are heterotetramers composed of ...Excitatory neurotransmission meditated by glutamate receptors including N-methyl-D-aspartate receptors (NMDARs) is pivotal to brain development and function. NMDARs are heterotetramers composed of GluN1 and GluN2 subunits, which bind glycine and glutamate, respectively, to activate their ion channels. Despite importance in brain physiology, the precise mechanisms by which activation and inhibition occur via subunit-specific binding of agonists and antagonists remain largely unknown. Here, we show the detailed patterns of conformational changes and inter-subunit and -domain reorientation leading to agonist-gating and subunit-dependent competitive inhibition by providing multiple structures in distinct ligand states at 4 Å or better. The structures reveal that activation and competitive inhibition by both GluN1 and GluN2 antagonists occur by controlling the tension of the linker between the ligand-binding domain and the transmembrane ion channel of the GluN2 subunit. Our results provide detailed mechanistic insights into NMDAR pharmacology, activation, and inhibition, which are fundamental to the brain physiology.
External links	Cell / PubMed:32610085 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.092 - 4.39 Å
Structure data	21673 6whr EMDB-21673, PDB-6whr: GluN1b-GluN2B NMDA receptor in non-active 2 conformation at 4 angstrom resolution Method: EM (single particle) / Resolution: 3.99 Å 21674 6whs EMDB-21674, PDB-6whs: GluN1b-GluN2B NMDA receptor in non-active 1 conformation at 3.95 angstrom resolution Method: EM (single particle) / Resolution: 4.0 Å 21675 6wht EMDB-21675, PDB-6wht: GluN1b-GluN2B NMDA receptor in active conformation at 4.4 angstrom resolution Method: EM (single particle) / Resolution: 4.39 Å 21676 6whu EMDB-21676, PDB-6whu: GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 1 Method: EM (single particle) / Resolution: 3.93 Å 21677 6whv EMDB-21677, PDB-6whv: GluN1b-GluN2B NMDA receptor in complex with SDZ 220-040 and L689,560, class 2 Method: EM (single particle) / Resolution: 4.05 Å 21678 6whw EMDB-21678, PDB-6whw: GluN1b-GluN2B NMDA receptor in complex with GluN2B antagonist SDZ 220-040, class 1 Method: EM (single particle) / Resolution: 4.09 Å 21679 6whx EMDB-21679, PDB-6whx: GluN1b-GluN2B NMDA receptor in complex with GluN2B antagonist SDZ 220-040, class 2 Method: EM (single particle) / Resolution: 4.09 Å 21680 6why EMDB-21680, PDB-6why: GluN1b-GluN2B NMDA receptor in complex with GluN1 antagonist L689,560, class 1 Method: EM (single particle) / Resolution: 4.03 Å 21681 6wi0 EMDB-21681, PDB-6wi0: GluN1b-GluN2B NMDA receptor in complex with GluN1 antagonist L689,560, class 2 Method: EM (single particle) / Resolution: 4.27 Å 21682 6wi1 EMDB-21682, PDB-6wi1: GluN1b-GluN2B NMDA receptor in active conformation stabilized by inter-GluN1b-GluN2B subunit cross-linking Method: EM (single particle) / Resolution: 3.62 Å PDB-6usu: Crystal structure of GluN1/GluN2A ligand-binding domain in complex with L689,560 and glutamate Method: X-RAY DIFFRACTION / Resolution: 2.092 Å PDB-6usv: Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and SDZ 220-040 Method: X-RAY DIFFRACTION / Resolution: 2.304 Å
Chemicals	ChemComp-QGM: (2R,4S)-5,7-dichloro-4-[(phenylcarbamoyl)amino]-1,2,3,4-tetrahydroquinoline-2-carboxylic acid ChemComp-GLU: GLUTAMIC ACID / Glutamic acid ChemComp-HOH: WATER / Water ChemComp-GLY: GLYCINE / Glycine ChemComp-QGP: (2S)-2-amino-3-[2',4'-dichloro-4-hydroxy-5-(phosphonomethyl)biphenyl-3-yl]propanoic acid ChemComp-GOL: GLYCEROL / Glycerol ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine
Source	rattus norvegicus (Norway rat)
Keywords	METAL TRANSPORT / NMDARs / LBD / Ion channels / MEMBRANE PROTEIN / Ligand-gated ion channels / Ionotropic glutamate receptor / GluN1 antagonist / GluN2B antagonist