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- EMDB-63228: Alpha-7 nicotinic acetylcholine receptor bound to inhibitory bicy... -

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Basic information

Entry
Database: EMDB / ID: EMD-63228
TitleAlpha-7 nicotinic acetylcholine receptor bound to inhibitory bicyclic peptide KP2007 in a resting state.
Map data
Sample
  • Complex: Alpha-7 nicotinic acetylcholine receptor bound to inhibitory bicyclic peptide KP2007 in a resting state.
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
    • Protein or peptide: Inhibitory bicyclic peptide KP2007
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordsnicotinic acetylcholine receptor / 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 / chloride channel regulator activity / acetylcholine-gated monoatomic cation-selective channel activity ...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 / chloride channel regulator activity / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory / cation channel complex / acetylcholine binding / dendritic spine organization / 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 / modulation of excitatory postsynaptic potential / negative regulation of tumor necrosis factor production / plasma membrane raft / monoatomic ion channel activity / toxic substance binding / monoatomic ion transport / negative regulation of cytokine production involved in inflammatory response / positive regulation of excitatory postsynaptic potential / negative regulation of canonical NF-kappaB signal transduction / positive regulation of long-term synaptic potentiation / response to nicotine / excitatory postsynaptic potential / regulation of membrane potential / synapse organization / cognition / calcium channel activity / memory / positive regulation of angiogenesis / intracellular calcium ion homeostasis / calcium ion transport / transmembrane signaling receptor activity / amyloid-beta binding / monoatomic ion transmembrane transport / chemical synaptic transmission / learning or memory / postsynaptic membrane / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / neuron projection / postsynapse / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsChen H / Sun D / Tian C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22227810 China
CitationJournal: To Be Published
Title: De novo discovery of unnatural and potent conotoxin-like bicyclic peptides through a phage-encoded library
Authors: Cao X / Chen H / Wang X / Yang X / Wang T / Zhou L / Shi C / Liu S / Liu L / Tian C / Sun D
History
DepositionJan 20, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63228.png

Downloads & links

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Map

FileDownload / File: emd_63228.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.)
1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å		1.07 Å/pix.
x 240 pix.
= 256.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.8071471 - 3.4768412
Average (Standard dev.)0.0076824953 (±0.090835445)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 256.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63228_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63228_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63228_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Sample components

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Entire : Alpha-7 nicotinic acetylcholine receptor bound to inhibitory bicy...

EntireName: Alpha-7 nicotinic acetylcholine receptor bound to inhibitory bicyclic peptide KP2007 in a resting state.
Components
  • Complex: Alpha-7 nicotinic acetylcholine receptor bound to inhibitory bicyclic peptide KP2007 in a resting state.
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
    • Protein or peptide: Inhibitory bicyclic peptide KP2007
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Alpha-7 nicotinic acetylcholine receptor bound to inhibitory bicy...

SupramoleculeName: Alpha-7 nicotinic acetylcholine receptor bound to inhibitory bicyclic peptide KP2007 in a resting state.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 56.505176 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 EAVSKDFA

UniProtKB: Neuronal acetylcholine receptor subunit alpha-7

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Macromolecule #2: Inhibitory bicyclic peptide KP2007

MacromoleculeName: Inhibitory bicyclic peptide KP2007 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 2.085413 KDa
SequenceString:
PACCEGNWCR WLRLDTCG

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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: 5 / 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 K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.1 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: EMDB MAP
EMDB ID:

31168

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65264
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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