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- PDB-7koo: Alpha-7 nicotinic acetylcholine receptor bound to alpha-bungaroto... -

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Basic information

Entry
Database: PDB / ID: 7koo
TitleAlpha-7 nicotinic acetylcholine receptor bound to alpha-bungarotoxin in a resting state
Components
  • Alpha-bungarotoxin isoform V31
  • Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusion
KeywordsMEMBRANE PROTEIN / Cys-loop receptor
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 / acetylcholine receptor inhibitor 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 / acetylcholine receptor inhibitor activity / positive regulation of CoA-transferase activity / ion channel regulator 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 / electron transport chain / synapse organization / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / calcium ion transport / amyloid-beta binding / toxin activity / monoatomic ion transmembrane transport / postsynaptic membrane / postsynapse / positive regulation of MAPK cascade / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / learning or memory / response to hypoxia / neuron projection / iron ion binding / positive regulation of protein phosphorylation / heme binding / positive regulation of cell population proliferation / synapse / signal transduction / protein homodimerization activity / extracellular region / membrane / plasma membrane
Similarity search - Function
Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Nicotinic acetylcholine receptor / Snake toxin-like superfamily / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain ...Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Nicotinic acetylcholine receptor / Snake toxin-like superfamily / 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
Soluble cytochrome b562 / Neuronal acetylcholine receptor subunit alpha-7 / Alpha-bungarotoxin isoform V31
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
Bungarus multicinctus (many-banded krait)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 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_entity_assembly ...atom_site / em_entity_assembly / em_software / entity / entity_poly / entity_poly_seq / pdbx_branch_scheme / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr / software / struct / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_entity_assembly.source / _em_software.category ..._em_entity_assembly.source / _em_software.category / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _pdbx_branch_scheme.asym_id / _pdbx_branch_scheme.auth_mon_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_branch_scheme.entity_id / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.num / _pdbx_branch_scheme.pdb_asym_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_branch_scheme.pdb_seq_num / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entity_branch_link.atom_id_2 / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_link.comp_id_2 / _pdbx_entity_branch_link.entity_branch_list_num_1 / _pdbx_entity_branch_link.entity_branch_list_num_2 / _pdbx_entity_branch_link.entity_id / _pdbx_entity_branch_link.leaving_atom_id_2 / _pdbx_entity_branch_list.comp_id / _pdbx_entity_branch_list.entity_id / _pdbx_entity_branch_list.num / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly_prop.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _software.version / _struct.pdbx_descriptor / _struct_asym.entity_id / _struct_conf.beg_label_asym_id / _struct_conf.end_label_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_comp_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_comp_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_seq_align_beg_ins_code / _struct_ref_seq.pdbx_seq_align_end_ins_code / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands
Description: Sequence discrepancy
Details: As noted for 7KOQ and 7KOX, two amino acids are different between our sequence, derived from P36544, and the literature referenced sequence, which was used for building the model (U40583.1). ...Details: As noted for 7KOQ and 7KOX, two amino acids are different between our sequence, derived from P36544, and the literature referenced sequence, which was used for building the model (U40583.1). Please correct S35 and S111. Thanks!
Provider: author / Type: Coordinate replacement
Revision 2.1May 12, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.current_status / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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
F: Alpha-bungarotoxin isoform V31
G: Alpha-bungarotoxin isoform V31
H: Alpha-bungarotoxin isoform V31
I: Alpha-bungarotoxin isoform V31
J: Alpha-bungarotoxin isoform V31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,94330
Polymers357,77110
Non-polymers7,17220
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, This assembly was also confirmed by electrophysiology in cells.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area48390 Å2
ΔGint-196 kcal/mol
Surface area102510 Å2

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Components

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Protein , 2 types, 10 molecules ABCDEFGHIJ

#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 / Cell line (production host): GnTi- / Production host: Homo sapiens (human) / Strain (production host): HEK / Variant (production host): 293 / References: UniProt: P36544, UniProt: P0ABE7
#2: Protein
Alpha-bungarotoxin isoform V31 / BGTX V31 / Long neurotoxin 1


Mass: 7721.973 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Bungarus multicinctus (many-banded krait) / References: UniProt: P60616

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Sugars , 3 types, 15 molecules

#3: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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
#5: 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


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

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Non-polymers , 1 types, 5 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Ca

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Details

Has ligand of interestN
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Complex between alpha-bungarotoxin and the human alpha-7 nicotinic acetylcholine receptorCOMPLEX#1-#20MULTIPLE SOURCES
2Neuronal acetylcholine receptor subunit alpha-7,Soluble cytochrome b562 fusionCOMPLEX#11RECOMBINANT
3Alpha-bungarotoxin isoform V31COMPLEX#21RECOMBINANT
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 FIELD
Image recordingElectron dose: 61 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19_4080: / Classification: refinement
EM softwareName: RELION / Version: 3.1 / Category: initial Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 792521 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0119415
ELECTRON MICROSCOPYf_angle_d1.10626450
ELECTRON MICROSCOPYf_dihedral_angle_d13.6347080
ELECTRON MICROSCOPYf_chiral_restr0.0893090
ELECTRON MICROSCOPYf_plane_restr0.0073250

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