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- PDB-7eki: human alpha 7 nicotinic acetylcholine receptor in apo-form -

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Basic information

Entry
Database: PDB / ID: 7eki
Titlehuman alpha 7 nicotinic acetylcholine receptor in apo-form
ComponentsNeuronal acetylcholine receptor subunit alpha-7
KeywordsMEMBRANE PROTEIN / alpha 7 / nicotinic acetylcholine receptor / apo-form
Function / homology
Function and homology information


sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / short-term memory / regulation of amyloid fibril formation / positive regulation of CoA-transferase activity / acetylcholine receptor activity / dendritic spine organization ...sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / short-term memory / regulation of amyloid fibril formation / positive regulation of CoA-transferase activity / acetylcholine receptor activity / dendritic spine organization / chloride channel regulator activity / acetylcholine binding / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / acetylcholine-gated monoatomic cation-selective channel activity / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / plasma membrane raft / modulation of excitatory postsynaptic potential / response to amyloid-beta / positive regulation of excitatory postsynaptic potential / negative regulation of tumor necrosis factor production / toxic substance binding / monoatomic ion transport / monoatomic ion transmembrane transport / positive regulation of protein metabolic process / positive regulation of long-term synaptic potentiation / synapse organization / response to nicotine / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / monoatomic ion channel activity / amyloid-beta binding / postsynapse / postsynaptic membrane / positive regulation of MAPK cascade / learning or memory / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / neuron projection / positive regulation of protein phosphorylation / synapse / positive regulation of cell population proliferation / 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
CHOLESTEROL / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsLiu, S. / Zhao, Y. / Sun, D. / Tian, C.
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 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: Neuronal acetylcholine receptor subunit alpha-7
B: Neuronal acetylcholine receptor subunit alpha-7
C: Neuronal acetylcholine receptor subunit alpha-7
D: Neuronal acetylcholine receptor subunit alpha-7
E: Neuronal acetylcholine receptor subunit alpha-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,68720
Polymers282,5265
Non-polymers5,16115
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area36290 Å2
ΔGint-179 kcal/mol
Surface area85580 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 23 through 136 or resid 138 through 621))
d_2ens_1(chain "B" and (resid 23 through 136 or resid 138 through 621))
d_3ens_1(chain "C" and (resid 23 through 136 or resid 138 through 621))
d_4ens_1(chain "D" and (resid 23 through 136 or resid 138 through 621))
d_5ens_1(chain "E" and (resid 23 through 136 or resid 138 through 621))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYGLYA1 - 114
d_12ens_1CYSALAA116 - 395
d_13ens_1NAGNAGF
d_14ens_1NAGNAGF
d_15ens_1NAGNAGK
d_16ens_1CLRCLRL
d_21ens_1GLYGLYB1 - 114
d_22ens_1CYSALAB116 - 395
d_23ens_1NAGNAGG
d_24ens_1NAGNAGG
d_25ens_1NAGNAGM
d_26ens_1CLRCLRN
d_31ens_1GLYGLYC1 - 114
d_32ens_1CYSALAC116 - 395
d_33ens_1NAGNAGH
d_34ens_1NAGNAGH
d_35ens_1NAGNAGO
d_36ens_1CLRCLRP
d_41ens_1GLYGLYD1 - 114
d_42ens_1CYSALAD116 - 395
d_43ens_1NAGNAGI
d_44ens_1NAGNAGI
d_45ens_1NAGNAGQ
d_46ens_1CLRCLRR
d_51ens_1GLYGLYE1 - 114
d_52ens_1CYSALAE116 - 395
d_53ens_1NAGNAGJ
d_54ens_1NAGNAGJ
d_55ens_1NAGNAGS
d_56ens_1CLRCLRT

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Components

#1: Protein
Neuronal acetylcholine receptor subunit alpha-7


Mass: 56505.176 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA7, NACHRA7 / Production host: Homo sapiens (human) / References: UniProt: P36544
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H46O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human alpha7 nicotinic acetylcholine receptor / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19_4092refinement
PHENIX1.19_4092refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73466 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 81.59 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002816455
ELECTRON MICROSCOPYf_angle_d0.57322490
ELECTRON MICROSCOPYf_chiral_restr0.03972620
ELECTRON MICROSCOPYf_plane_restr0.00332760
ELECTRON MICROSCOPYf_dihedral_angle_d12.2585795
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000813284690571
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000694853534202
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000630936776884
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.000869306641213

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