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- EMDB-22980: Alpha-7 nicotinic acetylcholine receptor bound to epibatidine in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-22980
TitleAlpha-7 nicotinic acetylcholine receptor bound to epibatidine in a desensitized state
Map dataAlpha-7 nicotinic acetylcholine receptor bound to epibatidine in a desensitized state
Sample
  • Complex: alpha 7 nicotinic receptor in complex with the agonist epibatidine
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: EPIBATIDINE
  • Ligand: CALCIUM ION
KeywordsCys-loop receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / acetylcholine-gated monoatomic cation-selective channel activity / cation channel complex ...sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / acetylcholine-gated monoatomic cation-selective channel activity / cation channel complex / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / neurotransmitter receptor complex / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / modulation of excitatory postsynaptic potential / response to amyloid-beta / monoatomic ion channel activity / positive regulation of protein metabolic process / negative regulation of tumor necrosis factor production / plasma membrane raft / positive regulation of excitatory postsynaptic potential / toxic substance binding / monoatomic ion transport / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / positive regulation of long-term synaptic potentiation / regulation of membrane potential / excitatory postsynaptic potential / response to nicotine / synapse organization / electron transport chain / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / transmembrane signaling receptor activity / amyloid-beta binding / monoatomic ion transmembrane transport / chemical synaptic transmission / postsynaptic membrane / periplasmic space / learning or memory / electron transfer activity / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / postsynapse / positive regulation of MAPK cascade / neuron projection / iron ion binding / positive regulation of cell population proliferation / synapse / heme binding / dendrite / signal transduction / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor ...Nicotinic acetylcholine receptor / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
Soluble cytochrome b562 / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsNoviello CM / Hibbs RE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NS095899 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NS077983 United States
CitationJournal: Cell / Year: 2021
Title: Structure and gating mechanism of the α7 nicotinic acetylcholine receptor.
Authors: Colleen M Noviello / Anant Gharpure / Nuriya Mukhtasimova / Rico Cabuco / Leah Baxter / Dominika Borek / Steven M Sine / Ryan E Hibbs /
Abstract: The α7 nicotinic acetylcholine receptor plays critical roles in the central nervous system and in the cholinergic inflammatory pathway. This ligand-gated ion channel assembles as a homopentamer, is ...The α7 nicotinic acetylcholine receptor plays critical roles in the central nervous system and in the cholinergic inflammatory pathway. This ligand-gated ion channel assembles as a homopentamer, is exceptionally permeable to Ca, and desensitizes faster than any other Cys-loop receptor. The α7 receptor has served as a prototype for the Cys-loop superfamily yet has proven refractory to structural analysis. We present cryo-EM structures of the human α7 nicotinic receptor in a lipidic environment in resting, activated, and desensitized states, illuminating the principal steps in the gating cycle. The structures also reveal elements that contribute to its function, including a C-terminal latch that is permissive for channel opening, and an anionic ring in the extracellular vestibule that contributes to its high conductance and calcium permeability. Comparisons among the α7 structures provide a foundation for mapping the gating cycle and reveal divergence in gating mechanisms in the Cys-loop receptor superfamily.
History
DepositionNov 9, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7koq
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22980.png

Downloads & links

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Map

FileDownload / File: emd_22980.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAlpha-7 nicotinic acetylcholine receptor bound to epibatidine in a desensitized state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.67 Å/pix.
x 416 pix.
= 277.472 Å		0.67 Å/pix.
x 416 pix.
= 277.472 Å		0.67 Å/pix.
x 416 pix.
= 277.472 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.05932636 - 0.11512535
Average (Standard dev.)-0.000000000000004 (±0.0022678245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 277.472 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6670.6670.667
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z277.472277.472277.472
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ416416416
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS416416416
D min/max/mean-0.0590.115-0.000

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Supplemental data

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Half map: Alpha-7 nicotinic acetylcholine receptor bound to epibatidine in...

Fileemd_22980_half_map_1.map
AnnotationAlpha-7 nicotinic acetylcholine receptor bound to epibatidine in a desensitized state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Alpha-7 nicotinic acetylcholine receptor bound to epibatidine in...

Fileemd_22980_half_map_2.map
AnnotationAlpha-7 nicotinic acetylcholine receptor bound to epibatidine in a desensitized state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : alpha 7 nicotinic receptor in complex with the agonist epibatidine

EntireName: alpha 7 nicotinic receptor in complex with the agonist epibatidine
Components
  • Complex: alpha 7 nicotinic receptor in complex with the agonist epibatidine
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: EPIBATIDINE
  • Ligand: CALCIUM ION

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Supramolecule #1: alpha 7 nicotinic receptor in complex with the agonist epibatidine

SupramoleculeName: alpha 7 nicotinic receptor in complex with the agonist epibatidine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrom...

MacromoleculeName: Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.832293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EFQRKLYKEL VKNYNPLERP VANDSQPLTV YFSLSLLQIM DVDEKNQVLT TNIWLQMSWT DHYLQWNVSE YPGVKTVRFP DGQIWKPDI LLYNSADERF DATFHTNVLV NSSGHCQYLP PGIFKSSCYI DVRWFPFDVQ HCKLKFGSWS YGGWSLDLQM Q EADISGYI ...String:
EFQRKLYKEL VKNYNPLERP VANDSQPLTV YFSLSLLQIM DVDEKNQVLT TNIWLQMSWT DHYLQWNVSE YPGVKTVRFP DGQIWKPDI LLYNSADERF DATFHTNVLV NSSGHCQYLP PGIFKSSCYI DVRWFPFDVQ HCKLKFGSWS YGGWSLDLQM Q EADISGYI PNGEWDLVGI PGKRSERFYE CCKEPYPDVT FTVTMRRRTL YYGLNLLIPC VLISALALLV FLLPADSGEK IS LGITVLL SLTVFMLLVA EIMPATSDSV PLIAQYFAST MIIVGLSVVV TVIVLQYHHH DPDGGKMPKW TRVILLNWCA WFL RMKRPG EDKVRPACQH KQRRCSLASV EMAGAMADLE DNWETLNDNL KVIEKADNAA QVKDALTKMR AAALDAQKAT PPKL EDKSP DSPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLCGRMACS PTHDEHLLHG GQPPE GDPD LAKILEEVRY IANRFRCQDE SEAVCSEWKF AACVVDRLCL MAFSVFTIIC TIGILMSAPN FVEAVSKDFA WSHPQF EK

UniProtKB: Neuronal acetylcholine receptor subunit alpha-7, Soluble cytochrome b562, Neuronal acetylcholine receptor subunit alpha-7

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: EPIBATIDINE

MacromoleculeName: EPIBATIDINE / type: ligand / ID: 4 / Number of copies: 5 / Formula: EPJ
Molecular weightTheoretical: 208.687 Da
Chemical component information

ChemComp-EPJ:
EPIBATIDINE / alkaloid*YM

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Details: Resolve CryoEM Density Modification, FSC=0.5 / Number images used: 1790185
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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