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Structure paper

TitleConformational diversity and fully opening mechanism of native NMDA receptor
Journal, issue, pagesTo Be Published
Publish dateApr 22, 2025 (structure data deposition date)
AuthorsYu J / Xu RS / Ge JP
External linksSearch PubMed
MethodsEM (single particle)
Resolution2.98 - 6.37 Å
Structure data

EMDB-64277: native GluN1/N2B receptor in the fully open state
Method: EM (single particle) / Resolution: 3.37 Å

EMDB-64278: native GluN1/N2B receptor in the open state TMD focused map
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-64279: native GluN1/N2A/N2B-s1 consensus map in the closed state
Method: EM (single particle) / Resolution: 2.98 Å

EMDB-64280: native GluN1/N2A/N2B-s1-TMD focused map in the closed state
Method: EM (single particle) / Resolution: 3.37 Å

EMDB-64281: native GluN1/N2A/N2B-subtype2 consensus map in the closed state
Method: EM (single particle) / Resolution: 3.27 Å

EMDB-64283: native GluN1/N2A/N2B-S2-TMD focused map in the closed state
Method: EM (single particle) / Resolution: 3.39 Å

EMDB-64284: native GluN1/N2A-subtype 1-TMD focused
Method: EM (single particle) / Resolution: 4.29 Å

EMDB-64285: native GluN1/N2B-subtype1 in closed state
Method: EM (single particle) / Resolution: 3.93 Å

EMDB-64289: native GluN1/N2A-subtype2-consensus map
Method: EM (single particle) / Resolution: 6.37 Å

EMDB-64290: native GluN1/N2A-subtype2-TMD focused map
Method: EM (single particle) / Resolution: 4.53 Å

EMDB-64292: native GluN1/N2A-S3-consensus map in the closed state
Method: EM (single particle) / Resolution: 3.29 Å

EMDB-64294: native GluN1/N2A-S3 TMD focused map in the closed state
Method: EM (single particle) / Resolution: 3.73 Å

EMDB-64295: native GluN1/N2B receptor consensus map in the closed state
Method: EM (single particle) / Resolution: 3.37 Å

EMDB-64296: native GluN1/N2B-TMD-focused map in the closed state
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-64297: native GluN1/N2B/NX-consensus map in the closed state
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-64298: native GluN1/N2A/NX-TMD-focused map in the closed state
Method: EM (single particle) / Resolution: 4.22 Å

EMDB-64299: native GluN1/N2B/NX composite map in the closed state
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-64300: native GluN1_N2A_NX_subtype-consensus map in the closed state
Method: EM (single particle) / Resolution: 3.58 Å

EMDB-64301: native GluN1_N2A_NX_subtype1_TMD_focused map in the closed state
Method: EM (single particle) / Resolution: 3.58 Å

EMDB-64302: native GluN1_N2A_NX_subtype1_composite_map in the closed state
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-64303: native GluN1_N2A_NX_S2_consensus map
Method: EM (single particle) / Resolution: 3.66 Å

EMDB-64304: native GluN1_N2A_NX_subtype2_TMD_focused
Method: EM (single particle) / Resolution: 3.94 Å

EMDB-64305: native GluN1_N2A_NX_subtype2_composite map
Method: EM (single particle) / Resolution: 3.66 Å

EMDB-64306: native GluN1_NX_consensus_map
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-64307: native GluN1_NX TMD focused map
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-64308: native GluN1_GluNX composite map
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-64309: native native NMDA receptor-GluN1/N2B in inactive state TMD focused map
Method: EM (single particle) / Resolution: 4.55 Å

EMDB-64310: native NMDA receptor-GluN1/N2B in the inactive state consensus map
Method: EM (single particle) / Resolution: 6.21 Å

EMDB-64311: native NMDA receptor-GluN1/N2A in inactive state consensus map
Method: EM (single particle) / Resolution: 3.55 Å

EMDB-64313: native NMDA receptor-GluN1/N2A/N2B in inactive state consensus map
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-64314: native NMDA receptor-GluN1/N2A/N2B in inactive state TMD focused map
Method: EM (single particle) / Resolution: 3.24 Å

EMDB-64315: native NMDA receptor-GluN1/N2B/NX in the open state consensus map
Method: EM (single particle) / Resolution: 3.28 Å

EMDB-64316: native NMDA receptor-GluN1/N2B/NX in the open state TMD focused map
Method: EM (single particle) / Resolution: 3.42 Å

EMDB-64317: native NMDA receptor-GluN1/N2B/NX in the open state
Method: EM (single particle) / Resolution: 3.28 Å

EMDB-64318: native NMDA receptor-GluN1/N2A in inactive state TMD focused map
Method: EM (single particle) / Resolution: 3.53 Å

EMDB-64319: native NMDA receptor-GluN1/N2B/NX in inactive state consensus map
Method: EM (single particle) / Resolution: 3.47 Å

EMDB-64320: native NMDA receptor-GluN1/N2B/NX in inactive state TMD focused map
Method: EM (single particle) / Resolution: 3.56 Å

EMDB-64321: native NMDA receptor-GluN1/N2B/NX in inactive state
Method: EM (single particle) / Resolution: 3.47 Å

EMDB-64326: native NMDA receptor-GluN1-N2A-NX consensus map
Method: EM (single particle) / Resolution: 3.23 Å

EMDB-64327: native NMDA receptor-GlUN1/N2A/NX TMD focused map
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-64328: native NMDA receptor-GluN1/N2A/NX composite map
Method: EM (single particle) / Resolution: 3.23 Å

EMDB-64330: native NMDA receptor-GluN1/NX consensus map
Method: EM (single particle) / Resolution: 3.57 Å

EMDB-64331: native NMDA receptor-GluN1/NX TMD focused map
Method: EM (single particle) / Resolution: 3.51 Å

EMDB-64332: native NMDA receptor-GluN1/NX composite map
Method: EM (single particle) / Resolution: 3.57 Å

64337

9un2

EMDB-64337, PDB-9un2:
native NMDAR receptor-GluN1/N2B in the inactive state
Method: EM (single particle) / Resolution: 4.3 Å

64338

9un3

EMDB-64338, PDB-9un3:
native NMDA receptor-GluN1/N2B in the open state
Method: EM (single particle) / Resolution: 3.37 Å

64353

9unj

EMDB-64353, PDB-9unj:
native NMDA receptor-GluN1/N2A-S1 in closed state
Method: EM (single particle) / Resolution: 3.93 Å

64354

9unk

EMDB-64354, PDB-9unk:
native NMDA receptor-GluN1/N2B in the closed state
Method: EM (single particle) / Resolution: 3.37 Å

64356

9unm

EMDB-64356, PDB-9unm:
native NMDA receptor-GluN1/N2A-S2 in the closed state
Method: EM (single particle) / Resolution: 6.37 Å

64357

9unn

EMDB-64357, PDB-9unn:
native NMDA receptor-GluN1/N2A-S3 in the closed state
Method: EM (single particle) / Resolution: 3.29 Å

64358

9uno

EMDB-64358, PDB-9uno:
native NMDA receptor-GluN1/N2A in the inactive state
Method: EM (single particle) / Resolution: 3.55 Å

64359

9unp

EMDB-64359, PDB-9unp:
native NMDA receptor-GluN1/N2A/N2B-S2 in the closed state
Method: EM (single particle) / Resolution: 3.27 Å

64360

9unq

EMDB-64360, PDB-9unq:
native NMDA receptor-GluN1/N2A/2B in inactive state
Method: EM (single particle) / Resolution: 3.2 Å

64361

9unr

EMDB-64361, PDB-9unr:
native NMDA receptor-GluN1/N2A/N2B-S1 in the closed state
Method: EM (single particle) / Resolution: 2.98 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-GLY:
GLYCINE

ChemComp-GLU:
GLUTAMIC ACID

ChemComp-JC9:
(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one / antidepressant*YM

Source
  • mus musculus (house mouse)
  • Homo sapiens (human)
KeywordsMEMBRANE PROTEIN / native / NMDA receptor / ionotropic ion channel / excitatory neurotransmitter / MEMBRANE / open state / inotropic ion channel / MEMBRANE PROTEIN/IMMUNE SYSTEM / ion channel / MEMBRANE PROTEIN-IMMUNE SYSTEM complex

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