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- EMDB-31176: human alpha 7 nicotinic acetylcholine receptor bound to EVP-6124 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-31176
Titlehuman alpha 7 nicotinic acetylcholine receptor bound to EVP-6124 and PNU-120596
Map data
Sample
  • Complex: Human alpha7 nicotinic acetylcholine receptor bound to EVP-6124 and PNU-120596
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: 7-chloro-N-(quinuclidin-3-yl)benzo[b]thiophene-2-carboxamide
  • Ligand: N-(5-Chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea
Keywordsalpha 7 / nicotinic acetylcholine receptor / agonist / PAM / MEMBRANE PROTEIN
Function / homology
Function and homology information


sensory processing / dendrite arborization / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity ...sensory processing / dendrite arborization / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / regulation of amyloid fibril formation / short-term memory / positive regulation of CoA-transferase activity / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / plasma membrane raft / modulation of excitatory postsynaptic potential / response to amyloid-beta / monoatomic ion channel activity / negative regulation of tumor necrosis factor production / positive regulation of excitatory postsynaptic potential / toxic substance binding / monoatomic ion transport / positive regulation of protein metabolic process / positive regulation of long-term synaptic potentiation / response to nicotine / synapse organization / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / amyloid-beta binding / monoatomic ion transmembrane transport / postsynaptic membrane / postsynapse / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / learning or memory / response to hypoxia / neuron projection / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / synapse / 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: 3.02 Å
AuthorsLiu S / Zhao Y
CitationJournal: Cell Res / Year: 2021
Title: Structural basis of human α7 nicotinic acetylcholine receptor activation.
Authors: Yue Zhao / Sanling Liu / Yingxin Zhou / Mengge Zhang / Haopeng Chen / H Eric Xu / Demeng Sun / Lei Liu / Changlin Tian /
History
DepositionApr 6, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ekt
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31176.png

Downloads & links

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Map

FileDownload / File: emd_31176.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.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å		1.01 Å/pix.
x 240 pix.
= 243.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32 / Movie #1: 0.4
Minimum - Maximum-1.5733471 - 2.9668517
Average (Standard dev.)0.009994924 (±0.094141215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 243.36002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z243.360243.360243.360
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-1.5732.9670.010

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Supplemental data

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Sample components

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Entire : Human alpha7 nicotinic acetylcholine receptor bound to EVP-6124 a...

EntireName: Human alpha7 nicotinic acetylcholine receptor bound to EVP-6124 and PNU-120596
Components
  • Complex: Human alpha7 nicotinic acetylcholine receptor bound to EVP-6124 and PNU-120596
    • Protein or peptide: Neuronal acetylcholine receptor subunit alpha-7
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CHOLESTEROL
  • Ligand: 7-chloro-N-(quinuclidin-3-yl)benzo[b]thiophene-2-carboxamide
  • Ligand: N-(5-Chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea

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Supramolecule #1: Human alpha7 nicotinic acetylcholine receptor bound to EVP-6124 a...

SupramoleculeName: Human alpha7 nicotinic acetylcholine receptor bound to EVP-6124 and PNU-120596
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: 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 #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / 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 #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 5 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #5: 7-chloro-N-(quinuclidin-3-yl)benzo[b]thiophene-2-carboxamide

MacromoleculeName: 7-chloro-N-(quinuclidin-3-yl)benzo[b]thiophene-2-carboxamide
type: ligand / ID: 5 / Number of copies: 5 / Formula: I33
Molecular weightTheoretical: 320.837 Da
Chemical component information

ChemComp-I33:
7-chloro-N-(quinuclidin-3-yl)benzo[b]thiophene-2-carboxamide / agonist*YM

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Macromolecule #6: N-(5-Chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea

MacromoleculeName: N-(5-Chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea
type: ligand / ID: 6 / Number of copies: 5 / Formula: I34
Molecular weightTheoretical: 311.721 Da
Chemical component information

ChemComp-I34:
N-(5-Chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 62.0 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46899
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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