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- PDB-7koq: Alpha-7 nicotinic acetylcholine receptor bound to epibatidine in ... -

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Basic information

Entry
Database: PDB / ID: 7koq
TitleAlpha-7 nicotinic acetylcholine receptor bound to epibatidine in a desensitized state
ComponentsNeuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
KeywordsMEMBRANE PROTEIN / Cys-loop receptor
Function / homology
Function and homology information


sensory processing / dendrite arborization / acetylcholine receptor activity / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / regulation of amyloid fibril formation / acetylcholine-gated channel complex / positive regulation of CoA-transferase activity / short-term memory / regulation of amyloid precursor protein catabolic process ...sensory processing / dendrite arborization / acetylcholine receptor activity / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / regulation of amyloid fibril formation / acetylcholine-gated channel complex / positive regulation of CoA-transferase activity / short-term memory / regulation of amyloid precursor protein catabolic process / acetylcholine-gated monoatomic cation-selective channel activity / synaptic transmission, cholinergic / chloride channel regulator activity / dendritic spine organization / acetylcholine binding / acetylcholine receptor signaling pathway / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / modulation of excitatory postsynaptic potential / plasma membrane raft / positive regulation of excitatory postsynaptic potential / response to amyloid-beta / negative regulation of tumor necrosis factor production / toxic substance binding / monoatomic ion transport / positive regulation of protein metabolic process / monoatomic ion transmembrane transport / response to nicotine / positive regulation of long-term synaptic potentiation / synapse organization / calcium channel activity / intracellular calcium ion homeostasis / memory / cognition / positive regulation of angiogenesis / calcium ion transport / monoatomic ion channel activity / amyloid-beta binding / postsynaptic membrane / postsynapse / positive regulation of MAPK cascade / electron transfer activity / periplasmic space / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / learning or memory / neuron projection / positive regulation of protein phosphorylation / iron ion binding / synapse / positive regulation of cell population proliferation / heme binding / 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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor ...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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
EPIBATIDINE / Soluble cytochrome b562 / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsNoviello, C.M. / Hibbs, R.E. / Gharpure, A. / Mukhtasimova, N. / Cabuco, R. / Baxter, L. / Borek, D. / Sine, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NS095899 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NS077983 United States
CitationJournal: Cell / Year: 2021
Title: Structure and gating mechanism of the α7 nicotinic acetylcholine receptor.
Authors: Colleen M Noviello / Anant Gharpure / Nuriya Mukhtasimova / Rico Cabuco / Leah Baxter / Dominika Borek / Steven M Sine / Ryan E Hibbs /
Abstract: The α7 nicotinic acetylcholine receptor plays critical roles in the central nervous system and in the cholinergic inflammatory pathway. This ligand-gated ion channel assembles as a homopentamer, is ...The α7 nicotinic acetylcholine receptor plays critical roles in the central nervous system and in the cholinergic inflammatory pathway. This ligand-gated ion channel assembles as a homopentamer, is exceptionally permeable to Ca, and desensitizes faster than any other Cys-loop receptor. The α7 receptor has served as a prototype for the Cys-loop superfamily yet has proven refractory to structural analysis. We present cryo-EM structures of the human α7 nicotinic receptor in a lipidic environment in resting, activated, and desensitized states, illuminating the principal steps in the gating cycle. The structures also reveal elements that contribute to its function, including a C-terminal latch that is permissive for channel opening, and an anionic ring in the extracellular vestibule that contributes to its high conductance and calcium permeability. Comparisons among the α7 structures provide a foundation for mapping the gating cycle and reveal divergence in gating mechanisms in the Cys-loop receptor superfamily.
History
DepositionNov 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0May 5, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: atom_site / em_software ...atom_site / em_software / entity / entity_poly / entity_poly_seq / pdbx_branch_scheme / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr / software / struct / struct_conn / struct_mon_prot_cis / struct_ref_seq_dif / struct_sheet_range
Item: _em_software.category / _entity.formula_weight ..._em_software.category / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _software.version / _struct.pdbx_descriptor / _struct_conn.pdbx_dist_value / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Sequence discrepancy
Details: As noted in 7KOX, there are two amino acids that need to be changed; S35 and S111. The original residues were N and P, respectively. Thanks! Colleen
Provider: author / Type: Coordinate replacement
Revision 2.1May 12, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

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Assembly

Deposited unit
A: Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
B: Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
C: Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
D: Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
E: Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,73930
Polymers319,1615
Non-polymers5,57825
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area38430 Å2
ΔGint-190 kcal/mol
Surface area89220 Å2

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Components

#1: Protein
Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion / Cytochrome b-562


Mass: 63832.293 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: CHRNA7, NACHRA7, cybC / Production host: Homo sapiens (human) / References: UniProt: P36544, UniProt: P0ABE7
#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.: 10 / 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-EPJ / EPIBATIDINE / (2R)-2-(6-CHLOROPYRIDIN-3-YL)-7-AZABICYCLO[2.2.1]HEPTANE / Epibatidine


Mass: 208.687 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H13ClN2 / Comment: alkaloid*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
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: alpha 7 nicotinic receptor in complex with the agonist epibatidine
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
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: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4080: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: OTHER / Num. of particles: 1790185 / Details: Resolve CryoEM Density Modification, FSC=0.5 / Symmetry type: POINT
RefinementHighest resolution: 3.6 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01416565
ELECTRON MICROSCOPYf_angle_d0.81122580
ELECTRON MICROSCOPYf_dihedral_angle_d12.2045930
ELECTRON MICROSCOPYf_chiral_restr0.0952600
ELECTRON MICROSCOPYf_plane_restr0.0052775

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