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- EMDB-18596: nicotinic acetylcholine receptor in intact synaptic membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-18596
Titlenicotinic acetylcholine receptor in intact synaptic membrane
Map dataMap of acetylcholine receptor in membrane obtained from aligned volumes in helical reconstructions of tubular vesicles having different diameters and symmetry (see e.g. EMD-14942)
Sample
  • Organelle or cellular component: Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane
    • Protein or peptide: Acetylcholine receptor subunit alpha
    • Protein or peptide: Acetylcholine receptor subunit delta
    • Protein or peptide: Acetylcholine receptor subunit beta
    • Protein or peptide: Acetylcholine receptor subunit gamma
KeywordsIon channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


acetylcholine-gated monoatomic cation-selective channel activity / transmembrane signaling receptor activity / postsynaptic membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha / Acetylcholine receptor subunit beta / Acetylcholine receptor subunit gamma / Acetylcholine receptor subunit delta
Similarity search - Component
Biological speciesTorpedo marmorata (marbled electric ray) / Tetronarce californica (Pacific electric ray)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsUnwin N
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MC_U105184294 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Influence of lipid bilayer on the structure of the muscle-type nicotinic acetylcholine receptor.
Authors: Nigel Unwin /
Abstract: The muscle-type nicotinic acetylcholine receptor is a transmitter-gated ion channel residing in the plasma membrane of electrocytes and striated muscle cells. It is present predominantly at synaptic ...The muscle-type nicotinic acetylcholine receptor is a transmitter-gated ion channel residing in the plasma membrane of electrocytes and striated muscle cells. It is present predominantly at synaptic junctions, where it effects rapid depolarization of the postsynaptic membrane in response to acetylcholine released into the synaptic cleft. Previously, cryo-EM of intact membrane from revealed that the lipid bilayer surrounding the junctional receptor has a uniquely asymmetric and ordered structure, due to a high concentration of cholesterol. It is now shown that this special lipid environment influences the transmembrane (TM) folding of the protein. All five submembrane MX helices of the membrane-intact junctional receptor align parallel to the surface of the cholesterol-ordered lipids in the inner leaflet of the bilayer; also, the TM helices in the outer leaflet are splayed apart. However in the structure obtained from the same protein after extraction and incorporation in nanodiscs, the MX helices do not align to a planar surface, and the TM helices arrange compactly in the outer leaflet. Realignment of the MX helices of the nanodisc-solved structure to a planar surface converts their adjoining TM helices into an obligatory splayed configuration, characteristic of the junctional receptor. Thus, the form of the receptor sustained by the special lipid environment of the synaptic junction is the one that mediates fast synaptic transmission; whereas, the nanodisc-embedded protein may be like the extrajunctional form, existing in a disordered lipid environment.
History
DepositionOct 5, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18596.png

Downloads & links

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Map

FileDownload / File: emd_18596.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of acetylcholine receptor in membrane obtained from aligned volumes in helical reconstructions of tubular vesicles having different diameters and symmetry (see e.g. EMD-14942)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 200 pix.
= 268. Å		1.34 Å/pix.
x 200 pix.
= 268. Å		1.34 Å/pix.
x 200 pix.
= 268. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0005
Minimum - Maximum-0.0007659927 - 0.0014821306
Average (Standard dev.)0.000031837724 (±0.00016353911)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin2985670
Dimensions200200200
Spacing200200200
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: First half map

Fileemd_18596_half_map_1.map
AnnotationFirst half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map

Fileemd_18596_half_map_2.map
AnnotationSecond half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Muscle-type nicotinic acetylcholine receptor in intact synaptic m...

EntireName: Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane
Components
  • Organelle or cellular component: Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane
    • Protein or peptide: Acetylcholine receptor subunit alpha
    • Protein or peptide: Acetylcholine receptor subunit delta
    • Protein or peptide: Acetylcholine receptor subunit beta
    • Protein or peptide: Acetylcholine receptor subunit gamma

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Supramolecule #1: Muscle-type nicotinic acetylcholine receptor in intact synaptic m...

SupramoleculeName: Muscle-type nicotinic acetylcholine receptor in intact synaptic membrane
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Postsynaptic membranes were isolated from fresh electric organ and incubated in low salt buffer to form ordered arrays of acetylcholine receptors in tubular vesicles
Source (natural)Organism: Torpedo marmorata (marbled electric ray)
Molecular weightTheoretical: 290 KDa

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Macromolecule #1: Acetylcholine receptor subunit alpha

MacromoleculeName: Acetylcholine receptor subunit alpha / type: protein_or_peptide / ID: 1
Details: The extracellular domain is excluded from this analysis
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 50.168164 KDa
SequenceString: 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

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Macromolecule #2: Acetylcholine receptor subunit delta

MacromoleculeName: Acetylcholine receptor subunit delta / type: protein_or_peptide / ID: 2
Details: The extracellular domain is excluded from this analysis
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 57.625711 KDa
SequenceString: 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

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Macromolecule #3: Acetylcholine receptor subunit beta

MacromoleculeName: Acetylcholine receptor subunit beta / type: protein_or_peptide / ID: 3
Details: The extracellular domain is excluded from this analysis
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 53.731773 KDa
SequenceString: 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

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Macromolecule #4: Acetylcholine receptor subunit gamma

MacromoleculeName: Acetylcholine receptor subunit gamma / type: protein_or_peptide / ID: 4
Details: The extracellular domain is excluded from this analysis
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetronarce californica (Pacific electric ray)
Molecular weightTheoretical: 56.335684 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
100.0 mMC2H7AsO2sodium cacodylate
1.0 mMCaCl2calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 20 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AMYLAMINE
Details: Grids were washed extensively in chloroform and coated with additional carbon before use
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: HOMEMADE PLUNGER
DetailsSpecimen comprises tubular vesicles which are imaged in thin ice over holes in the support film

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.8000000000000003 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 104478 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
DetailsAll images taken manually: by searching at low magnification for long straight and narrow tubes, then recording in integrating mode
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 200 / Number real images: 4045 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Details: Images were collected in integrating mode, 2 seconds exposure
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 160652
Details: 160652 tube segments from 4045 selected micrographs were reduced to 107524 tube segments after 2D classification
Startup modelType of model: OTHER
Details: Original model was a map of the tube obtained by Fourier-Bessel reconstruction
Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 34 / Avg.num./class: 3162 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionNumber classes used: 34 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1)
Details: The volumes for FSC determination were cut out from helical reconstructions of each class average
Number images used: 107524
DetailsImages of appropriate helical families were selected on the basis of their FFTs, then drift-corrected and dose-weighted

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7smm

chain_id: A, residue_range: 212-433, source_name: PDB, initial_model_type: experimental modelinitial model is of complete protein, PDB entry 7smm

7smm

chain_id: B, residue_range: 226-479, source_name: PDB, initial_model_type: experimental modelinitial model is of complete protein, PDB entry 7smm

7smm

chain_id: C, residue_range: 218-460, source_name: PDB, initial_model_type: experimental modelinitial model is of complete protein, PDB entry 7smm

7smm

chain_id: D, residue_range: 212-433, source_name: PDB, initial_model_type: experimental modelinitial model is of complete protein, PDB entry 7smm

7smm

chain_id: E, residue_range: 220-472, source_name: PDB, initial_model_type: experimental modelinitial model is of complete protein, PDB entry 7smm
DetailsRefinement parameters were chosen to minimise changes to the original secondary structure
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 350
Output model

PDB-8qqm:
nicotinic acetylcholine receptor in intact synaptic membrane

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