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Yorodumi- EMDB-14048: Torpedo muscle-type nicotinic acetylcholine receptor - Resting co... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14048 | |||||||||
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Title | Torpedo muscle-type nicotinic acetylcholine receptor - Resting conformation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | pentameric ligand-gated ion channel / nicotinic receptor / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information acetylcholine-gated monoatomic cation-selective channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynaptic membrane / neuron projection Similarity search - Function | |||||||||
Biological species | Tetronarce californica (Pacific electric ray) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Zarkadas E / Pebay-Peyroula E | |||||||||
Funding support | European Union, Canada, 2 items
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Citation | Journal: Neuron / Year: 2022 Title: Conformational transitions and ligand-binding to a muscle-type nicotinic acetylcholine receptor. Authors: Eleftherios Zarkadas / Eva Pebay-Peyroula / Mackenzie John Thompson / Guy Schoehn / Tomasz Uchański / Jan Steyaert / Christophe Chipot / Francois Dehez / John Edward Baenziger / Hugues Nury / Abstract: Fast synaptic communication requires receptors that respond to the presence of neurotransmitter by opening an ion channel across the post-synaptic membrane. The muscle-type nicotinic acetylcholine ...Fast synaptic communication requires receptors that respond to the presence of neurotransmitter by opening an ion channel across the post-synaptic membrane. The muscle-type nicotinic acetylcholine receptor from the electric fish, Torpedo, is the prototypic ligand-gated ion channel, yet the structural changes underlying channel activation remain undefined. Here we use cryo-EM to solve apo and agonist-bound structures of the Torpedo nicotinic receptor embedded in a lipid nanodisc. Using both a direct biochemical assay to define the conformational landscape and molecular dynamics simulations to assay flux through the pore, we correlate structures with functional states and elucidate the motions that lead to pore activation of a heteromeric nicotinic receptor. We highlight an underappreciated role for the complementary subunit in channel gating, establish the structural basis for the differential agonist affinities of α/δ versus α /γ sites, and explain why nicotine is less potent at muscle nicotinic receptors compared to neuronal ones. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_14048.map.gz | 59.4 MB | EMDB map data format | |
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Header (meta data) | emd-14048-v30.xml emd-14048.xml | 23.6 KB 23.6 KB | Display Display | EMDB header |
Images | emd_14048.png | 75.1 KB | ||
Masks | emd_14048_msk_1.map emd_14048_msk_2.map | 64 MB 64 MB | Mask map | |
Filedesc metadata | emd-14048.cif.gz | 7.1 KB | ||
Others | emd_14048_additional_1.map.gz emd_14048_additional_2.map.gz emd_14048_half_map_1.map.gz emd_14048_half_map_2.map.gz | 56.9 MB 32.4 MB 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14048 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14048 | HTTPS FTP |
-Validation report
Summary document | emd_14048_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_14048_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_14048_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_14048_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14048 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14048 | HTTPS FTP |
-Related structure data
Related structure data | 7qkoMC 7ql5C 7ql6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14048.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.145 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_14048_msk_1.map | ||||||||||||
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Density Histograms |
-Mask #2
File | emd_14048_msk_2.map | ||||||||||||
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-Additional map: DeepEMhanced map
File | emd_14048_additional_1.map | ||||||||||||
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Annotation | DeepEMhanced map | ||||||||||||
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-Additional map: Unsharpened map
File | emd_14048_additional_2.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
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Density Histograms |
-Half map: Half map A
File | emd_14048_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
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Density Histograms |
-Half map: Half map B
File | emd_14048_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Torpedo muscle-type nicotinic acetylcholine receptor
Entire | Name: Torpedo muscle-type nicotinic acetylcholine receptor |
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Components |
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-Supramolecule #1: Torpedo muscle-type nicotinic acetylcholine receptor
Supramolecule | Name: Torpedo muscle-type nicotinic acetylcholine receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: Native receptor reconstituted in lipidic nanodiscs. |
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Source (natural) | Organism: Tetronarce californica (Pacific electric ray) |
Molecular weight | Theoretical: 250 KDa |
-Macromolecule #1: Acetylcholine receptor subunit alpha
Macromolecule | Name: Acetylcholine receptor subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Tetronarce californica (Pacific electric ray) |
Molecular weight | Theoretical: 50.168164 KDa |
Sequence | String: SEHETRLVAN LLENYNKVIR PVEHHTHFVD ITVGLQLIQL ISVDEVNQIV ETNVRLRQQW IDVRLRWNPA DYGGIKKIRL PSDDVWLPD LVLYNNADGD FAIVHMTKLL LDYTGKIMWT PPAIFKSYCE IIVTHFPFDQ QNCTMKLGIW TYDGTKVSIS P ESDRPDLS ...String: SEHETRLVAN LLENYNKVIR PVEHHTHFVD ITVGLQLIQL ISVDEVNQIV ETNVRLRQQW IDVRLRWNPA DYGGIKKIRL PSDDVWLPD LVLYNNADGD FAIVHMTKLL LDYTGKIMWT PPAIFKSYCE IIVTHFPFDQ QNCTMKLGIW TYDGTKVSIS P ESDRPDLS TFMESGEWVM KDYRGWKHWV YYTCCPDTPY LDITYHFIMQ RIPLYFVVNV IIPCLLFSFL TGLVFYLPTD SG EKMTLSI SVLLSLTVFL LVIVELIPST SSAVPLIGKY MLFTMIFVIS SIIITVVVIN THHRSPSTHT MPQWVRKIFI DTI PNVMFF STMKRASKEK QENKIFADDI DISDISGKQV TGEVIFQTPL IKNPDVKSAI EGVKYIAEHM KSDEESSNAA EEWK YVAMV IDHILLCVFM LICIIGTVSV FAGRLIELSQ EG UniProtKB: Acetylcholine receptor subunit alpha |
-Macromolecule #2: Acetylcholine receptor subunit beta
Macromolecule | Name: Acetylcholine receptor subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tetronarce californica (Pacific electric ray) |
Molecular weight | Theoretical: 53.731773 KDa |
Sequence | String: SVMEDTLLSV LFETYNPKVR PAQTVGDKVT VRVGLTLTNL LILNEKIEEM TTNVFLNLAW TDYRLQWDPA AYEGIKDLRI PSSDVWQPD IVLMNNNDGS FEITLHVNVL VQHTGAVSWQ PSAIYRSSCT IKVMYFPFDW QNCTMVFKSY TYDTSEVTLQ H ALDAKGER ...String: SVMEDTLLSV LFETYNPKVR PAQTVGDKVT VRVGLTLTNL LILNEKIEEM TTNVFLNLAW TDYRLQWDPA AYEGIKDLRI PSSDVWQPD IVLMNNNDGS FEITLHVNVL VQHTGAVSWQ PSAIYRSSCT IKVMYFPFDW QNCTMVFKSY TYDTSEVTLQ H ALDAKGER EVKEIVINKD AFTENGQWSI EHKPSRKNWR SDDPSYEDVT FYLIIQRKPL FYIVYTIIPC ILISILAILV FY LPPDAGE KMSLSISALL AVTVFLLLLA DKVPETSLSV PIIIRYLMFI MILVAFSVIL SVVVLNLHHR SPNTHTMPNW IRQ IFIETL PPFLWIQRPV TTPSPDSKPT IISRANDEYF IRKPAGDFVC PVDNARVAVQ PERLFSEMKW HLNGLTQPVT LPQD LKEAV EAIKYIAEQL ESASEFDDLK KDWQYVAMVA DRLFLYVFFV ICSIGTFSIF LDASHNVPPD NPFA UniProtKB: Acetylcholine receptor subunit beta |
-Macromolecule #3: Acetylcholine receptor subunit delta
Macromolecule | Name: Acetylcholine receptor subunit delta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tetronarce californica (Pacific electric ray) |
Molecular weight | Theoretical: 57.625711 KDa |
Sequence | String: VNEEERLIND LLIVNKYNKH VRPVKHNNEV VNIALSLTLS NLISLKETDE TLTSNVWMDH AWYDHRLTWN ASEYSDISIL RLPPELVWI PDIVLQNNND GQYHVAYFCN VLVRPNGYVT WLPPAIFRSS CPINVLYFPF DWQNCSLKFT ALNYDANEIT M DLMTDTID ...String: VNEEERLIND LLIVNKYNKH VRPVKHNNEV VNIALSLTLS NLISLKETDE TLTSNVWMDH AWYDHRLTWN ASEYSDISIL RLPPELVWI PDIVLQNNND GQYHVAYFCN VLVRPNGYVT WLPPAIFRSS CPINVLYFPF DWQNCSLKFT ALNYDANEIT M DLMTDTID GKDYPIEWII IDPEAFTENG EWEIIHKPAK KNIYPDKFPN GTNYQDVTFY LIIRRKPLFY VINFITPCVL IS FLASLAF YLPAESGEKM STAISVLLAQ AVFLLLTSQR LPETALAVPL IGKYLMFIMS LVTGVIVNCG IVLNFHFRTP STH VLSTRV KQIFLEKLPR ILHMSRADES EQPDWQNDLK LRRSSSVGYI SKAQEYFNIK SRSELMFEKQ SERHGLVPRV TPRI GFGNN NENIAASDQL HDEIKSGIDS TNYIVKQIKE KNAYDEEVGN WNLVGQTIDR LSMFIITPVM VLGTIFIFVM GNFNH PPAK PFEGDPFDYS SDHPRCA UniProtKB: Acetylcholine receptor subunit delta |
-Macromolecule #4: Acetylcholine receptor subunit gamma
Macromolecule | Name: Acetylcholine receptor subunit gamma / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Tetronarce californica (Pacific electric ray) |
Molecular weight | Theoretical: 56.335684 KDa |
Sequence | String: ENEEGRLIEK LLGDYDKRII PAKTLDHIID VTLKLTLTNL ISLNEKEEAL TTNVWIEIQW NDYRLSWNTS EYEGIDLVRI PSELLWLPD VVLENNVDGQ FEVAYYANVL VYNDGSMYWL PPAIYRSTCP IAVTYFPFDW QNCSLVFRSQ TYNAHEVNLQ L SAEEGEAV ...String: ENEEGRLIEK LLGDYDKRII PAKTLDHIID VTLKLTLTNL ISLNEKEEAL TTNVWIEIQW NDYRLSWNTS EYEGIDLVRI PSELLWLPD VVLENNVDGQ FEVAYYANVL VYNDGSMYWL PPAIYRSTCP IAVTYFPFDW QNCSLVFRSQ TYNAHEVNLQ L SAEEGEAV EWIHIDPEDF TENGEWTIRH RPAKKNYNWQ LTKDDTDFQE IIFFLIIQRK PLFYIINIIA PCVLISSLVV LV YFLPAQA GGQKCTLSIS VLLAQTIFLF LIAQKVPETS LNVPLIGKYL IFVMFVSMLI VMNCVIVLNV SLRTPNTHSL SEK IKHLFL GFLPKYLGMQ LEPSEETPEK PQPRRRSSFG IMIKAEEYIL KKPRSELMFE EQKDRHGLKR VNKMTSDIDI GTTV DLYKD LANFAPEIKS CVEACNFIAK STKEQNDSGS ENENWVLIGK VIDKACFWIA LLLFSIGTLA IFLTGHFNQV PEFPF PGDP RKYVP UniProtKB: Acetylcholine receptor subunit gamma |
-Macromolecule #9: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 9 / Number of copies: 9 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.65 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Details: Cryosparc Non-Uniform refinement / Number images used: 68038 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |