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- EMDB-82114: Alpha-7 nicotinic acetylcholine receptor bound to inhibitory bicy... -

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Basic information

Entry
Database: EMDB / ID: EMD-82114
TitleAlpha-7 nicotinic acetylcholine receptor bound to inhibitory bicyclic peptide KP1877 in a resting state
Map data
Sample
  • Complex: Human nicotinic acetylcholine receptor alpha-7 bound to synthetic inhibitory peptide KP1877
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
    • Protein or peptide: synthetic peptide KP1877
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordsnicotinic acetylcholine receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


sensory processing / dendrite arborization / synaptic transmission involved in micturition / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / chloride channel regulator activity / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity ...sensory processing / dendrite arborization / synaptic transmission involved in micturition / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / chloride channel regulator activity / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory / acetylcholine receptor signaling pathway / dendritic spine organization / acetylcholine binding / regulation of amyloid precursor protein catabolic process / positive regulation of amyloid-beta formation / synaptic transmission, cholinergic / response to amyloid-beta / negative regulation of amyloid-beta formation / positive regulation of protein metabolic process / negative regulation of tumor necrosis factor production / modulation of excitatory postsynaptic potential / plasma membrane raft / monoatomic ion channel activity / monoatomic ion transport / toxic substance binding / negative regulation of cytokine production involved in inflammatory response / excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / negative regulation of canonical NF-kappaB signal transduction / positive regulation of long-term synaptic potentiation / response to nicotine / memory / regulation of membrane potential / synapse organization / intracellular calcium ion homeostasis / cognition / positive regulation of angiogenesis / calcium channel activity / calcium ion transport / transmembrane signaling receptor activity / amyloid-beta binding / chemical synaptic transmission / monoatomic ion transmembrane transport / response to hypoxia / positive regulation of MAPK cascade / learning or memory / positive regulation of ERK1 and ERK2 cascade / postsynaptic membrane / postsynapse / neuron projection / 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: 2.71 Å
AuthorsChen H / Sun D / Tian C
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22227810 China
CitationJournal: Chem Commun (Camb) / Year: 2026
Title: Screening, synthesis and structural characterization of a novel bicyclic peptide inhibiting α7 nicotinic acetylcholine receptor.
Authors: Xichu Yang / Kele Cui / Xiuxiu Cao / Haopeng Chen / Changlin Tian / Demeng Sun /
Abstract: Peptides targeting the α7 nicotinic acetylcholine receptor (α7-nAChR) represent promising candidates for therapeutic and chemical probe development. Here, we identified a novel bicyclic peptide ...Peptides targeting the α7 nicotinic acetylcholine receptor (α7-nAChR) represent promising candidates for therapeutic and chemical probe development. Here, we identified a novel bicyclic peptide KP1877 phage-displayed peptide library screening followed by chemical synthesis of active analogs. Structural characterization reveals KP1877 adopts a unique bicyclic conformation distinct from known natural α7-nAChR-targeting peptides, and exerts potent inhibitory effect by stabilizing the closed, non-conducting state of the receptor orthosteric binding.
History
DepositionJul 15, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_82114.png

Downloads & links

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Map

FileDownload / File: emd_82114.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.5443994 - 2.7029037
Average (Standard dev.)0.0077697854 (±0.08666295)
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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Half map: #2

Fileemd_82114_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_82114_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human nicotinic acetylcholine receptor alpha-7 bound to synthetic...

EntireName: Human nicotinic acetylcholine receptor alpha-7 bound to synthetic inhibitory peptide KP1877
Components
  • Complex: Human nicotinic acetylcholine receptor alpha-7 bound to synthetic inhibitory peptide KP1877
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
    • Protein or peptide: synthetic peptide KP1877
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Human nicotinic acetylcholine receptor alpha-7 bound to synthetic...

SupramoleculeName: Human nicotinic acetylcholine receptor alpha-7 bound to synthetic inhibitory peptide KP1877
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: synthetic peptide KP1877

MacromoleculeName: synthetic peptide KP1877 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.658912 KDa
SequenceString:
GCGCRGGGWC WARGGCA

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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: PDB ENTRY
PDB model - PDB ID:

7eki

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 38353
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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