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- EMDB-63089: human alpha 7 nicotinic acetylcholine receptor in complex with L-... -

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Basic information

Entry
Database: EMDB / ID: EMD-63089
Titlehuman alpha 7 nicotinic acetylcholine receptor in complex with L-nicotine (four-nicotine-bound desensitized state)
Map data
Sample
  • Complex: human alpha 7 nicotinic acetylcholine receptor in complex with L-nicotine
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
  • Ligand: (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsLigand-gated ion channel / Nicotine / Desensitization / Recovery / Closed pore / MEMBRANE PROTEIN
Function / homology
Function and homology information


sensory processing / synaptic transmission involved in micturition / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory ...sensory processing / synaptic transmission involved in micturition / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory / cation channel complex / dendritic spine organization / chloride channel regulator activity / acetylcholine binding / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / neurotransmitter receptor complex / positive regulation of amyloid-beta formation / positive regulation of protein metabolic process / negative regulation of amyloid-beta formation / response to amyloid-beta / ligand-gated ion channel signaling pathway / monoatomic ion channel activity / modulation of excitatory postsynaptic potential / plasma membrane raft / negative regulation of tumor necrosis factor production / 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 / calcium channel activity / cognition / memory / 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 / learning or memory / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / postsynapse / neuron projection / positive regulation of MAPK cascade / positive regulation of cell population proliferation / dendrite / synapse / endoplasmic reticulum membrane / signal transduction / protein homodimerization activity / membrane / plasma 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
Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsLiu S / Chen H / Tian C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural insights into the progressive recovery from nicotine-induced desensitization of alpha7 nicotinic acetylcholine receptor
Authors: Liu S / Chen H / Zhu X / Ye F / Zhao Y / Qin J / Zheng Y / Wang X / Zhang L / Chen H / Li X / Mu W / Luo C / Hou H / Bai C / Liu L / Tian C
History
DepositionJan 11, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63089.png

Downloads & links

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Map

FileDownload / File: emd_63089.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 240 pix.
= 242.4 Å		1.01 Å/pix.
x 240 pix.
= 242.4 Å		1.01 Å/pix.
x 240 pix.
= 242.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.65774196 - 1.7966241
Average (Standard dev.)-0.00009367087 (±0.0673325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 242.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: map sharp

Fileemd_63089_additional_1.map
Annotationmap_sharp
Projections & Slices
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Histogram

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Half map: #2

Fileemd_63089_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63089_half_map_2.map
Projections & Slices
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Sample components

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Entire : human alpha 7 nicotinic acetylcholine receptor in complex with L-...

EntireName: human alpha 7 nicotinic acetylcholine receptor in complex with L-nicotine
Components
  • Complex: human alpha 7 nicotinic acetylcholine receptor in complex with L-nicotine
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
  • Ligand: (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: human alpha 7 nicotinic acetylcholine receptor in complex with L-...

SupramoleculeName: human alpha 7 nicotinic acetylcholine receptor in complex with L-nicotine
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

MacromoleculeName: Neuronal acetylcholine receptor subunit alpha-7 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.61625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRCSPGGVWL ALAASLLHVS LQGEFQRKLY KELVKNYNPL ERPVANDSQP LTVYFSLSLL QIMDVDEKNQ VLTTNIWLQM SWTDHYLQW NVSEYPGVKT VRFPDGQIWK PDILLYNSAD ERFDATFHTN VLVNSSGHCQ YLPPGIFKSS CYIDVRWFPF D VQHCKLKF ...String:
MRCSPGGVWL ALAASLLHVS LQGEFQRKLY KELVKNYNPL ERPVANDSQP LTVYFSLSLL QIMDVDEKNQ VLTTNIWLQM SWTDHYLQW NVSEYPGVKT VRFPDGQIWK PDILLYNSAD ERFDATFHTN VLVNSSGHCQ YLPPGIFKSS CYIDVRWFPF D VQHCKLKF GSWSYGGWSL DLQMQEADIS GYIPNGEWDL VGIPGKRSER FYECCKEPYP DVTFTVTMRR RTLYYGLNLL IP CVLISAL ALLVFLLPAD SGEKISLGIT VLLSLTVFML LVAEIMPATS DSVPLIAQYF ASTMIIVGLS VVVTVIVLQY HHH DPDGGK MPKWTRVILL NWCAWFLRMK RPGEDKVRPA CQHKQRRCSL ASVEMSAVAP PPASNGNLLY IGFRGLDGVH CVPT PDSGV VCGRMACSPT HDEHLLHGGQ PPEGDPDLAK ILEEVRYIAN RFRCQDESEA VCSEWKFAAC VVDRLCLMAF SVFTI ICTI GILMSAPNFV EAVSKDFAGG DYKDDDDK

UniProtKB: Neuronal acetylcholine receptor subunit alpha-7

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Macromolecule #3: (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE

MacromoleculeName: (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: NCT
Molecular weightTheoretical: 162.232 Da
Chemical component information

ChemComp-NCT:
(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.0 µm
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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31787
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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