8C2H: Glutamate receptor 1 flip isoform
Transmembrane domain of active state homomeric GluA1 AMPA receptor in tandem with TARP gamma 3. Determined by electron microscopy at 2.64 Å resolution. Released 30 Aug 2023.
- Method
- Electron microscopy
- Resolution
- 2.64 Å
- Organism
- Rattus norvegicus
- Chains
- 8
- Atoms
- 10,071
- Mol. weight
- 556.87 kDa
- Ligands
- POV, OLC, PLM
- Released
- 30 Aug 2023
Explore 8C2H in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8C2H contains 47 α-helices and 44 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 6 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 512-514 | 3 | |
| β-strand | 517 | 1 | 1 |
| α-helix | 519-540 | 22 | |
| α-helix | 569-580 | 12 | |
| α-helix | 592-620 | 29 | |
| α-helix | 781-782 | 2 | |
| β-strand | 783 | 1 | 2 |
| α-helix | 785-814 | 30 | |
Chain B: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 507-509 | 3 | |
| α-helix | 512-514 | 3 | |
| β-strand | 517 | 1 | 3 |
| α-helix | 519-540 | 22 | |
| α-helix | 569-580 | 12 | |
| α-helix | 592-613 | 22 | |
| α-helix | 616-620 | 5 | |
| β-strand | 783 | 1 | 1 |
| α-helix | 785-814 | 30 | |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 512-514 | 3 | |
| β-strand | 517 | 1 | 4 |
| α-helix | 519-540 | 22 | |
| α-helix | 569-580 | 12 | |
| α-helix | 592-620 | 29 | |
| β-strand | 783 | 1 | 3 |
| α-helix | 785-814 | 30 | |
Chain D: 8 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 503-505 | 3 | |
| β-strand | 506 | 1 | 5 |
| α-helix | 507-509 | 3 | |
| α-helix | 512-514 | 3 | |
| β-strand | 517 | 1 | 2 |
| α-helix | 519-542 | 24 | |
| α-helix | 569-580 | 12 | |
| α-helix | 592-613 | 22 | |
| α-helix | 616-620 | 5 | |
| β-strand | 624 | 1 | 5 |
| β-strand | 783 | 1 | 4 |
| α-helix | 785-814 | 30 | |
Chains E and G: 5 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-29 | 24 | |
| β-strand | 34-36 | 3 | 6 |
| β-strand | 37-38 | 2 | 7 |
| β-strand | 57-58 | 2 | 7 |
| β-strand | 59-61 | 3 | 6 |
| β-strand | 65-68 | 4 | 6 |
| β-strand | 74 | 1 | 8 |
| β-strand | 76 | 1 | 8 |
| β-strand | 77-79 | 3 | 6 |
| α-helix | 93-104 | 12 | |
| α-helix | 106-127 | 22 | |
| α-helix | 133-160 | 28 | |
| β-strand | 173-175 | 3 | 6 |
| α-helix | 177-206 | 30 | |
Chain F: 6 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-29 | 24 | |
| β-strand | 34-36 | 3 | 9 |
| β-strand | 37-38 | 2 | 10 |
| β-strand | 57-58 | 2 | 10 |
| β-strand | 59-61 | 3 | 9 |
| β-strand | 65-68 | 4 | 9 |
| β-strand | 74 | 1 | 11 |
| β-strand | 76 | 1 | 11 |
| β-strand | 77-79 | 3 | 9 |
| α-helix | 80 | 1 | |
| α-helix | 93-104 | 12 | |
| α-helix | 106-127 | 22 | |
| α-helix | 133-160 | 28 | |
| β-strand | 173-175 | 3 | 9 |
| α-helix | 177-206 | 30 | |
Chain H: 5 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-29 | 24 | |
| β-strand | 34-36 | 3 | 15 |
| β-strand | 37-38 | 2 | 16 |
| β-strand | 57-58 | 2 | 16 |
| β-strand | 59-61 | 3 | 15 |
| β-strand | 65-68 | 4 | 15 |
| β-strand | 77-79 | 3 | 15 |
| α-helix | 93-104 | 12 | |
| α-helix | 106-127 | 22 | |
| α-helix | 133-160 | 28 | |
| β-strand | 173-175 | 3 | 15 |
| α-helix | 177-206 | 30 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Glutamate receptor 1 flip isoform | A, B, C, D | protein | 915 | Rattus norvegicus | P19490 (AlphaFold model) |
| Voltage-dependent calcium channel gamma-3 subunit | E, F, G, H | protein | 314 | Rattus norvegicus | Q8VHX0 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D), FASTA
>8C2H_1 Glutamate receptor 1 flip isoform (chains A, B, C, D)
MPYIFAFFCTGFLGAVVGADYKDDDDKNFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEP
PKLLPQIDIVNISDSFEMTYRFCSQFSKGVYAIFGFYERRTVNMLTSFCGALHVCFITPS
FPVDTSNQFVLQLRPELQEALISIIDHYKWQTFVYIYDADRGLSVLQRVLDTAAEKNWQV
TAVNILTTTEEGYRMLFQDLEKKKERLVVVDCESERLNAILGQIVKLEKNGIGYHYILAN
LGFMDIDLNKFKESGANVTGFQLVNYTDTIPARIMQQWRTSDSRDHTRVDWKRPKYTSAL
TYDGVKVMAEAFQSLRRQRIDISRRGNAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGN
VQFNEKGRRTNYTLHVIEMKHDGIRKIGYWNEDDKFVPAATDAQAGGDNSSVQNRTYIVT
TILEDPYVMLKKNANQFEGNDRYEGYCVELAAEIAKHVGYSYRLEIVSDGKYGARDPDTK
AWNGMVGELVYGRADVAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFL
DPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHSEEFEEGRDQTTSDQSNEFGIFNSLW
FSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAED
LAKQTEIAYGTLEAGSTKEFFRRSKIAVFEKMWTYMKSAEPSVFVRTTEEGMIRVRKSKG
KYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSALRGPVNLAVLKLSEQGV
LDKLKSKWWYDKGECGSKDSGSKDKTSALSLSNVAGVFYILIGGLGLAMLVALIEFCYKS
RSESKRMKGFCLIPQQSINEAIRTSTLPRNSGAGASGGGGSGENGRVVSQDFPKSMQSIP
CMSHSSGMPLGATGL
Sequence of entity 2 (E, F, G, H), FASTA
>8C2H_2 Voltage-dependent calcium channel gamma-3 subunit (chains E, F, G, H)
RMCDRGIQMLITTVGAFAAFSLMTIAVGTDYWLYSRGVCRTKSTSDNETSRKNEEVMTHS
GLWRTCCLEGAFRGVCKKIDHFPEDADYEQDTAEYLLRAVRASSVFPILSVTLLFFGGLC
VAASEFHRSRHSVILSAGIFFVSAGLSNIIGIIVYISANAGDPGQRDSKKSYSYGWSFYF
GAFSFIIAEIVGVVAVHIYIEKHQQLRARSHSELLKKSTFARLPPYRYRFRRRSSSRSTE
PRSRDLSPISKGFHTIPSTDISMFTLSRDPSKLTMGTLLNSDRDHAFLQFHNSTPKEFKE
SLHNNPANRRTTPV
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| POV | (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl… | C42 H82 N O8 P | 2 |
| OLC | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate | C21 H40 O4 | 4 |
| PLM | Palmitic acid | C16 H32 O2 | 6 |
Primary citation
Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor. Zhang, D., Ivica, J., Krieger, J.M. et al. Nature (2023) 621:877-882. DOI 10.1038/s41586-023-06528-0 · PubMed
Other PDB entries of the same protein (UniProt P19490 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2AWW 2.21 Å, Synapse associated protein 97 PDZ2 domain variant C378G with C-terminal GluR-A peptide
- 3SAJ 2.5 Å, Crystal Structure of glutamate receptor GluA1 Amino Terminal Domain
- 8C2I 2.7 Å, Transmembrane domain of resting state homomeric GluA1 AMPA receptor in complex with TARP…
- 8AYN 2.8 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand LY3130481
- 8C1Q 2.82 Å, Resting state homomeric GluA1 AMPA receptor in complex with TARP gamma 3
- 8C1P 2.9 Å, Active state homomeric GluA1 AMPA receptor in complex with TARP gamma 3
- 7OCE 3.1 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and CNIH2 (LBD-TMD)
- 8AYL 3.2 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059
- 9OVU 3.2 Å, Composite map of GluA1/A2 in the activated state, in complex with positive allosteric…
- 9NR6 3.26 Å, The structure of Noelin 1 with cerebellar GluA1/A4-ATD
- 8AYM 3.3 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-55511118
- 8AYO 3.3 Å, Open state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059
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