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	Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 30, Issue 5, Page 629-639, Year 2023
Publish date	Mar 23, 2023
Authors	Jilin Zhang / Ming Zhang / Qinrui Wang / Han Wen / Zheyi Liu / Fangjun Wang / Yuhang Wang / Fenyong Yao / Nan Song / Zengwei Kou / Yang Li / Fei Guo / Shujia Zhu /
PubMed Abstract	N-methyl-D-aspartate (NMDA) receptors are heterotetramers comprising two GluN1 and two alternate GluN2 (N2A-N2D) subunits. Here we report full-length cryo-EM structures of the human N1-N2D di- ...N-methyl-D-aspartate (NMDA) receptors are heterotetramers comprising two GluN1 and two alternate GluN2 (N2A-N2D) subunits. Here we report full-length cryo-EM structures of the human N1-N2D di-heterotetramer (di-receptor), rat N1-N2C di-receptor and N1-N2A-N2C tri-heterotetramer (tri-receptor) at a best resolution of 3.0 Å. The bilobate N-terminal domain (NTD) in N2D intrinsically adopts a closed conformation, leading to a compact NTD tetramer in the N1-N2D receptor. Additionally, crosslinking the ligand-binding domain (LBD) of two N1 protomers significantly elevated the channel open probability (Po) in N1-N2D di-receptors. Surprisingly, the N1-N2C di-receptor adopted both symmetric (minor) and asymmetric (major) conformations, the latter further locked by an allosteric potentiator, PYD-106, binding to a pocket between the NTD and LBD in only one N2C protomer. Finally, the N2A and N2C subunits in the N1-N2A-N2C tri-receptor display a conformation close to one protomer in the N1-N2A and N1-N2C di-receptors, respectively. These findings provide a comprehensive structural understanding of diverse function in major NMDA receptor subtypes.
External links	Nat Struct Mol Biol / PubMed:36959261
Methods	EM (single particle)
Resolution	3.0 - 6.4 Å
Structure data	33788 7yff EMDB-33788, PDB-7yff: Structure of GluN1a-GluN2D NMDA receptor in complex with agonist glycine and competitive antagonist CPP. Method: EM (single particle) / Resolution: 3.6 Å 33789 7yfg EMDB-33789, PDB-7yfg: Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate (major class in asymmetry) Method: EM (single particle) / Resolution: 3.6 Å 33790 7yfh EMDB-33790, PDB-7yfh: Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine, glutamate and (R)-PYD-106 Method: EM (single particle) / Resolution: 3.0 Å 33791 7yfi EMDB-33791, PDB-7yfi: Structure of the Rat tri-heteromeric GluN1-GluN2A-GluN2C NMDA receptor in complex with glycine and glutamate Method: EM (single particle) / Resolution: 3.3 Å 33792 7yfl EMDB-33792, PDB-7yfl: Structure of GluN1a-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Method: EM (single particle) / Resolution: 3.9 Å 33793 7yfm EMDB-33793, PDB-7yfm: Structure of GluN1b-GluN2D NMDA receptor in complex with agonists glycine and glutamate. Method: EM (single particle) / Resolution: 5.1 Å 33795 7yfo EMDB-33795, PDB-7yfo: Structure of GluN1a E698C-GluN2D NMDA receptor in cystines crosslinked state. Method: EM (single particle) / Resolution: 6.4 Å 33798 7yfr EMDB-33798, PDB-7yfr: Structure of GluN1a E698C-GluN2D NMDA receptor in cystines non-crosslinked state. Method: EM (single particle) / Resolution: 5.1 Å 34674 8hdk EMDB-34674, PDB-8hdk: Structure of the Rat GluN1-GluN2C NMDA receptor in complex with glycine and glutamate (minor class in symmetry) Method: EM (single particle) / Resolution: 4.3 Å
Chemicals	ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine ChemComp-GLY: GLYCINE / Glycine ChemComp-7RC: (2R)-4-(3-phosphonopropyl)piperazine-2-carboxylic acid ChemComp-GLU: GLUTAMIC ACID / Glutamic acid ChemComp-IWB: methyl 4-[(2~{R})-3-ethanoyl-1-[2-(2-methyl-1~{H}-indol-3-yl)ethyl]-4-oxidanyl-5-oxidanylidene-2~{H}-pyrrol-2-yl]benzoate
Source	homo sapiens (human) rattus norvegicus (Norway rat)
Keywords	ELECTRON TRANSPORT / ion channel / cryo-EM structure / glutamate receptor / synaptic protein / MEMBRANE PROTEIN / NMDA receptor / GluN2C / GluN2A