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	Pre-activation and gating pathway of AMPA receptors revealed by full and partial agonists.
Journal, issue, pages	Nat Struct Mol Biol, Year 2026
Publish date	Sep 9, 2026
Authors	Thomas P Newton / Muhammed Aktolun / Maria V Yelshanskaya / Alexey A Alekseev / Laura Y Yen / Shanti Pal Gangwar / Ivan A Sobolevsky / Maria G Kurnikova / Alexander I Sobolevsky /
PubMed Abstract	AMPA receptors (AMPARs) mediate fast excitatory neurotransmission. Gating of AMPARs starts with agonist binding and transition into a non-conducting pre-active state, followed by transition into ...AMPA receptors (AMPARs) mediate fast excitatory neurotransmission. Gating of AMPARs starts with agonist binding and transition into a non-conducting pre-active state, followed by transition into conducting open or non-conducting desensitized states. While the terminal apo, open and desensitized states have been structurally characterized, the intermediate pre-active state has remained an enigma. Compared to full agonist glutamate, partial agonists reduce the maximal occupancy of the open state and increase the probability of the pre-active state occurrence. Here we use different partial agonists and time-resolved cryo-electron microscopy (cryo-EM) to capture a structural ensemble of GluA2-γ2 AMPAR complexes in the closed apo, pre-active, open and desensitized states. Binding of partial agonists to the ligand-binding domain (LBD) results in different extents of LBD clamshell closure, with closures exceeding a threshold of ~17° resulting in the open and desensitized states and smaller closures stabilizing the pre-active state. The pre-active state has a distinct gate conformation intermediate between the other two discrete states, completely open and closed. Combined with single-channel current recordings and molecular dynamics simulations, our structural results reveal the complete gating pathway of AMPARs and shed light on the molecular mechanisms of partial agonism and pre-activation.
External links	Nat Struct Mol Biol / PubMed:42717062
Methods	EM (single particle)
Resolution	2.74 - 4.72 Å
Structure data	76084 11vv EMDB-76084, PDB-11vv: GluA2-STZ apo state (full-length composite) Method: EM (single particle) / Resolution: 2.93 Å 76085 11vw EMDB-76085, PDB-11vw: GluA2-STZ desensitized state with partial agonist FW at 25 degrees C (full-length composite) Method: EM (single particle) / Resolution: 3.84 Å 76086 11vx EMDB-76086, PDB-11vx: GluA2-STZ open state with partial agonist FW at 25 degrees C (full-length composite) Method: EM (single particle) / Resolution: 3.37 Å 76087 11vy EMDB-76087, PDB-11vy: GluA2-STZ open state with partial agonist IW at 25 degrees C (full-length composite) Method: EM (single particle) / Resolution: 3.47 Å 76088 11vz EMDB-76088, PDB-11vz: GluA2-STZ pre-active state with partial agonist kainic acid (KA) at 25 degrees C (full-length composite) Method: EM (single particle) / Resolution: 3.98 Å 76089 11wa EMDB-76089, PDB-11wa: GluA2-STZ desensitized state with partial agonist NOW at 25 degrees C (full-length composite) Method: EM (single particle) / Resolution: 4.36 Å 76090 11wb EMDB-76090, PDB-11wb: GluA2-STZ open state with partial agonist NOW at 25 degrees C (full-length composite) Method: EM (single particle) / Resolution: 3.55 Å 76091 11wc EMDB-76091, PDB-11wc: GluA2-STZ pre-active state with partial agonist NOW at 25 degrees C (full-length composite) Method: EM (single particle) / Resolution: 4.02 Å 76092 11wd EMDB-76092, PDB-11wd: GluA2-STZ desensitized state with full agonist glutamate (Glu) at 25 degrees C (full-length composite) Method: EM (single particle) / Resolution: 3.69 Å 76093 11we EMDB-76093, PDB-11we: GluA2-STZ open state with full agonist glutamate (Glu) at 25 degrees C (full-length composite) Method: EM (single particle) / Resolution: 3.58 Å EMDB-76094: GluA2-STZ apo state (LBD-TMD only) Method: EM (single particle) / Resolution: 2.74 Å EMDB-76095: GluA2-STZ apo state (consensus) Method: EM (single particle) / Resolution: 3.12 Å EMDB-76096: GluA2-STZ desensitized state with partial agonist FW at 25 degrees C (ATD only) Method: EM (single particle) / Resolution: 3.95 Å EMDB-76097: GluA2-STZ desensitized state with partial agonist FW at 25 degrees C (LBD-TMD only) Method: EM (single particle) / Resolution: 3.73 Å EMDB-76098: GluA2-STZ desensitized state with partial agonist FW at 25 degrees C (consensus) Method: EM (single particle) / Resolution: 3.92 Å EMDB-76099: GluA2-STZ open state with partial agonist FW at 25 degrees C (ATD only) Method: EM (single particle) / Resolution: 3.44 Å EMDB-76100: GluA2-STZ open state with partial agonist FW at 25 degrees C (LBD-TMD only) Method: EM (single particle) / Resolution: 3.29 Å EMDB-76101: GluA2-STZ open state with partial agonist FW at 25 degrees C (consensus) Method: EM (single particle) / Resolution: 3.39 Å EMDB-76102: GluA2-STZ open state with partial agonist IW at 25 degrees C (ATD only) Method: EM (single particle) / Resolution: 3.64 Å EMDB-76103: GluA2-STZ open state with partial agonist IW at 25 degrees C (LBD-TMD only) Method: EM (single particle) / Resolution: 3.29 Å EMDB-76104: GluA2-STZ open state with partial agonist IW at 25 degrees C (consensus) Method: EM (single particle) / Resolution: 3.46 Å EMDB-76105: GluA2-STZ pre-active state with partial agonist kainic acid (KA) at 25 degrees C (ATD only) Method: EM (single particle) / Resolution: 3.98 Å EMDB-76106: GluA2-STZ pre-active state with partial agonist kainic acid (KA) at 25 degrees C (LBD-TMD only) Method: EM (single particle) / Resolution: 3.97 Å EMDB-76107: GluA2-STZ pre-active state with partial agonist kainic acid (KA) at 25 degrees C (consensus) Method: EM (single particle) / Resolution: 4.72 Å EMDB-76108: GluA2-STZ desensitized state with partial agonist NOW at 25 degrees C (ATD only) Method: EM (single particle) / Resolution: 4.3 Å EMDB-76109: GluA2-STZ desensitized state with partial agonist NOW at 25 degrees C (TMD only) Method: EM (single particle) / Resolution: 4.34 Å EMDB-76110: GluA2-STZ desensitized state with partial agonist NOW at 25 degrees C (consensus) Method: EM (single particle) / Resolution: 4.45 Å EMDB-76111: GluA2-STZ open state with partial agonist NOW at 25 degrees C (ATD only) Method: EM (single particle) / Resolution: 3.62 Å EMDB-76112: GluA2-STZ open state with partial agonist NOW at 25 degrees C (LBD-TMD only) Method: EM (single particle) / Resolution: 3.48 Å EMDB-76113: GluA2-STZ open state with partial agonist NOW at 25 degrees C (consensus) Method: EM (single particle) / Resolution: 3.57 Å EMDB-76114: GluA2-STZ pre-active state with partial agonist NOW at 25 degrees C (ATD only) Method: EM (single particle) / Resolution: 3.99 Å EMDB-76115: GluA2-STZ pre-active state with partial agonist NOW at 25 degrees C (LBD-TMD only) Method: EM (single particle) / Resolution: 4.04 Å EMDB-76116: GluA2-STZ pre-active state with partial agonist NOW at 25 degrees C (consensus) Method: EM (single particle) / Resolution: 3.99 Å EMDB-76117: GluA2-STZ desensitized state with full agonist glutamate (Glu) at 25 degrees C (ATD only) Method: EM (single particle) / Resolution: 3.84 Å EMDB-76118: GluA2-STZ desensitized state with full agonist glutamate (Glu) at 25 degrees C (LBD-TMD only) Method: EM (single particle) / Resolution: 3.71 Å EMDB-76119: GluA2-STZ desensitized state with full agonist glutamate (Glu) at 25 degrees C (consensus) Method: EM (single particle) / Resolution: 3.92 Å EMDB-76120: GluA2-STZ desensitized state with full agonist glutamate (Glu) at 25 degrees C (TMD only) Method: EM (single particle) / Resolution: 3.51 Å EMDB-76121: GluA2-STZ open state with full agonist glutamate (Glu) at 25 degrees C (ATD only) Method: EM (single particle) / Resolution: 3.74 Å EMDB-76122: GluA2-STZ open state with full agonist glutamate (Glu) at 25 degrees C (LBD-TMD only) Method: EM (single particle) / Resolution: 3.53 Å EMDB-76123: GluA2-STZ open state with full agonist glutamate (Glu) at 25 degrees C (consensus) Method: EM (single particle) / Resolution: 3.71 Å EMDB-76124: GluA2-STZ open state with full agonist glutamate (Glu) at 25 degrees C (TMD only) Method: EM (single particle) / Resolution: 3.46 Å
Chemicals	ChemComp-POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipidYM ChemComp-NA: Unknown entry ChemComp-FWD: 2-AMINO-3-(5-FLUORO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID ChemComp-SPD: SPERMIDINE ChemComp-IWD: 2-AMINO-3-(5-IODO-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-PROPIONIC ACID ChemComp-KAI: 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE ChemComp-NWD: 3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine ChemComp-GLU*: GLUTAMIC ACID
Source	rattus norvegicus (Norway rat) mus musculus (house mouse)
Keywords	MEMBRANE PROTEIN / ionotropic glutamate receptor (iGluR) / iGluR / GluA2 / transmembrane AMPAR regulatory protein (TARP) y2 / gamma2 / stargazin (STZ)