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	The open gate of the AMPA receptor forms a Ca binding site critical in regulating ion transport.
Journal, issue, pages	Nat Struct Mol Biol, Vol. 31, Issue 4, Page 688-700, Year 2024
Publish date	Feb 26, 2024
Authors	Terunaga Nakagawa / Xin-Tong Wang / Federico J Miguez-Cabello / Derek Bowie /
PubMed Abstract	Alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-propionic acid receptors (AMPARs) are cation-selective ion channels that mediate most fast excitatory neurotransmission in the brain. Although their gating ...Alpha-amino-3-hydroxyl-5-methyl-4-isoxazole-propionic acid receptors (AMPARs) are cation-selective ion channels that mediate most fast excitatory neurotransmission in the brain. Although their gating mechanism has been studied extensively, understanding how cations traverse the pore has remained elusive. Here we investigated putative ion and water densities in the open pore of Ca-permeable AMPARs (rat GRIA2 flip-Q isoform) at 2.3-2.6 Å resolution. We show that the ion permeation pathway attains an extracellular Ca binding site (site-G) when the channel gate moves into the open configuration. Site-G is highly selective for Ca over Na, favoring the movement of Ca into the selectivity filter of the pore. Seizure-related N619K mutation, adjacent to site-G, promotes channel opening but attenuates Ca binding and thus diminishes Ca permeability. Our work identifies the importance of site-G, which coordinates with the Q/R site of the selectivity filter to ensure the preferential transport of Ca through the channel pore.
External links	Nat Struct Mol Biol / PubMed:38409505
Methods	EM (single particle)
Resolution	2.29 - 5.59 Å
Structure data	29359 8fp4 EMDB-29359, PDB-8fp4: GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 500mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na610) Method: EM (single particle) / Resolution: 2.4 Å 29360 8fp9 EMDB-29360, PDB-8fp9: GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100mM glutamate (Open-CaNaMg) Method: EM (single particle) / Resolution: 2.44 Å 29361 8fpc EMDB-29361, PDB-8fpc: Conformation 1 of the ligand binding domain (LBDconf1) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100mM glutamate (Open-CaNaMg) Method: EM (single particle) / Resolution: 2.78 Å 29363 8fpg EMDB-29363, PDB-8fpg: GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100uM CNQX (Closed-CaNaMg) Method: EM (single particle) / Resolution: 2.32 Å 29364 8fph EMDB-29364, PDB-8fph: Conformation 2 of the ligand binding domain (LBDconf2) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100mM glutamate (Open-CaNaMg) Method: EM (single particle) / Resolution: 3.14 Å 29367 8fpk EMDB-29367, PDB-8fpk: LBD conformation 1 of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100uM CNQX (Closed-CaNaMg) Method: EM (single particle) / Resolution: 2.76 Å 29368 8fpl EMDB-29368, PDB-8fpl: LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100uM CNQX (Closed-CaNaMg) Method: EM (single particle) / Resolution: 2.81 Å 29369 8fps EMDB-29369, PDB-8fps: GluA2 flip Q isoform N619K mutant of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100mM glutamate (Open-CaNaMg/N619K) Method: EM (single particle) / Resolution: 2.38 Å 29370 8fpv EMDB-29370, PDB-8fpv: LBD conformation 1 (LBDconf1) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 500mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na610) Method: EM (single particle) / Resolution: 3.08 Å 29371 8fpy EMDB-29371, PDB-8fpy: LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 500mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na610) Method: EM (single particle) / Resolution: 2.98 Å 29372 8fpz EMDB-29372, PDB-8fpz: LBD conformation 3 (LBDconf3) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 500mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na610) Method: EM (single particle) / Resolution: 3.01 Å 29373 8fq1 EMDB-29373, PDB-8fq1: GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 150mM CaCl2, 330uM CTZ, and 100mM L-glutamate (Open-Ca150) Method: EM (single particle) / Resolution: 5.59 Å 29375 8fq2 EMDB-29375, PDB-8fq2: LBD conformation 1 (LBDconf1) of GluA2 flip Q isoform N619K mutant of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100mM glutamate (Open-CaNaMg/N619K) Method: EM (single particle) / Resolution: 3.14 Å 29376 8fq3 EMDB-29376, PDB-8fq3: LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform N619K mutant of AMPA receptor in complex with gain-of-function TARP gamma-2, with 10mM CaCl2, 150mM NaCl, 1mM MgCl2, 330uM CTZ, and 100mM glutamate (Open-CaNaMg/N619K) Method: EM (single particle) / Resolution: 3.17 Å 29378 8fq5 EMDB-29378, PDB-8fq5: GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 140mM NMDG, 330uM CTZ, and 100mM L-glutamate (Open-Na110) Method: EM (single particle) / Resolution: 2.34 Å 29379 8fq6 EMDB-29379, PDB-8fq6: LBD of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 150mM CaCl2, 330uM CTZ, and 100mM L-glutamate (Open-Ca150) Method: EM (single particle) / Resolution: 3.14 Å 29380 8fq8 EMDB-29380, PDB-8fq8: LBD conformation 1 (LBDconf1) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 140mM NMDG, 330uM CTZ, and 100mM L-glutamate (Open-Na110) Method: EM (single particle) / Resolution: 3.11 Å 29381 8fqa EMDB-29381, PDB-8fqa: LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 140mM NMDG, 330uM CTZ, and 100mM L-glutamate (Open-Na110) Method: EM (single particle) / Resolution: 3.35 Å 29382 8fqb EMDB-29382, PDB-8fqb: GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 10mM CaCl2, 140mM NMDG, 330uM CTZ, and 100mM L-glutamate (Open-Ca10) Method: EM (single particle) / Resolution: 2.36 Å 29384 8fqd EMDB-29384, PDB-8fqd: LBD conformation 1 (LBDconf1) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 10mM CaCl2, 140mM NMDG, 330uM CTZ, and 100mM L-glutamate (Open-Ca10) Method: EM (single particle) / Resolution: 3.01 Å 29385 8fqe EMDB-29385, PDB-8fqe: LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma2, with 10mM CaCl2, 140mM NMDG, 330uM CTZ, and 100mM L-glutamate (Open-Ca10) Method: EM (single particle) / Resolution: 3.14 Å 29386 8fqf EMDB-29386, PDB-8fqf: GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 150mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na260) Method: EM (single particle) / Resolution: 2.29 Å 29387 8fqg EMDB-29387, PDB-8fqg: LBD conformation 1 (LBDconf1) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 150mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na260) Method: EM (single particle) / Resolution: 3.01 Å 29388 8fqh EMDB-29388, PDB-8fqh: LBD conformation 2 (LBDconf2) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 150mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na260) Method: EM (single particle) / Resolution: 3.43 Å 29394 8fr0 EMDB-29394, PDB-8fr0: LBD conformation 3 (LBDconf3) of GluA2 flip Q isoform of AMPA receptor in complex with gain-of-function TARP gamma-2, with 150mM NaCl, 330uM CTZ, and 100mM glutamate (Open-Na260) Method: EM (single particle) / Resolution: 3.04 Å
Chemicals	ChemComp-CL: Unknown entry / Chloride ChemComp-HOH: WATER / Water ChemComp-CA: Unknown entry ChemComp-GLU: GLUTAMIC ACID / Glutamic acid ChemComp-CYZ: CYCLOTHIAZIDE / Cyclothiazide ChemComp, No image ChemComp-Y4Y: Unknown entry
Source	Rattus (rat) rattus norvegicus (Norway rat) mus musculus (house mouse)
Keywords	TRANSPORT PROTEIN / ionotropic glutamate receptor / ligand gated ion channel / AMPA receptor / TARP gamma-2 / ionotropic glutamate receptors / AMPA receptors / ion channel / ligand-gated ion channel / auxiliary subunit / stargazing / TARP gamma2 / Inotropic glutamate receptors / TARP / stargazin / glutamate / calcium / neurotransmitter receptor / synaptic transmission