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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 / synaptic transmission involved in micturition / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory ...sensory processing / synaptic transmission involved in micturition / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / acetylcholine-gated monoatomic cation-selective channel activity / short-term memory / cation channel complex / dendritic spine organization / chloride channel regulator activity / acetylcholine binding / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / neurotransmitter receptor complex / positive regulation of amyloid-beta formation / positive regulation of protein metabolic process / negative regulation of amyloid-beta formation / response to amyloid-beta / ligand-gated ion channel signaling pathway / monoatomic ion channel activity / modulation of excitatory postsynaptic potential / plasma membrane raft / negative regulation of tumor necrosis factor production / positive regulation of excitatory postsynaptic potential / toxic substance binding / monoatomic ion transport / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / positive regulation of long-term synaptic potentiation / response to nicotine / regulation of membrane potential / excitatory postsynaptic potential / synapse organization / calcium channel activity / cognition / memory / positive regulation of angiogenesis / intracellular calcium ion homeostasis / calcium ion transport / transmembrane signaling receptor activity / amyloid-beta binding / monoatomic ion transmembrane transport / chemical synaptic transmission / postsynaptic membrane / learning or memory / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / postsynapse / neuron projection / positive regulation of MAPK cascade / 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 / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 ...Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 / Distorted Sandwich / Mainly Beta
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.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
Revision 1.2Oct 23, 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
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Revision 2.0Dec 11, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
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Description: Atomic clashes
Details: The conformation of Pro158 was corrected from trans to cis.
Provider: author / Type: Coordinate replacement

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYGLYGLYAA23 - 13623 - 136
d_12CYSCYSALAALAAA138 - 502138 - 502
d_13NAGNAGNAGNAGAK601
d_14NAGNAGNAGNAGFF1
d_15NAGNAGNAGNAGFF2
d_16CLRCLRCLRCLRAL602
d_21GLYGLYGLYGLYBB23 - 13623 - 136
d_22CYSCYSALAALABB138 - 502138 - 502
d_23NAGNAGNAGNAGBM601
d_24NAGNAGNAGNAGGG1
d_25NAGNAGNAGNAGGG2
d_26CLRCLRCLRCLRBN602
d_31GLYGLYGLYGLYCC23 - 13623 - 136
d_32CYSCYSALAALACC138 - 502138 - 502
d_33NAGNAGNAGNAGCO601
d_34NAGNAGNAGNAGHH1
d_35NAGNAGNAGNAGHH2
d_36CLRCLRCLRCLRCP602
d_41GLYGLYGLYGLYDD23 - 13623 - 136
d_42CYSCYSALAALADD138 - 502138 - 502
d_43NAGNAGNAGNAGDQ601
d_44NAGNAGNAGNAGII1
d_45NAGNAGNAGNAGII2
d_46CLRCLRCLRCLRDR602
d_51GLYGLYGLYGLYEE23 - 13623 - 136
d_52CYSCYSALAALAEE138 - 502138 - 502
d_53NAGNAGNAGNAGES601
d_54NAGNAGNAGNAGJJ1
d_55NAGNAGNAGNAGJJ2
d_56CLRCLRCLRCLRET602

NCS oper:
IDCodeMatrixVector
1given(0.308501737507, 0.951223777214, 6.01519149573E-5), (-0.951223773541, 0.308501728236, 0.000127775985977), (0.000102986586298, -9.66370452172E-5, 0.999999990028)-31.4660202551, 199.065689438, 0.000278950634311
2given(-0.809425996879, 0.587221872252, 0.000168301716661), (-0.587221860386, -0.80942601437, 0.00011809449333), (0.000205575457204, -3.24169417487E-6, 0.999999978864)148.104164515, 290.450488578, -0.0486324087102
3given(-0.808627559236, -0.588320856108, 0.000201773976179), (0.58832088136, -0.808627559969, 9.90638927676E-5), (0.00010487864382, 0.000198813637318, 0.999999974737)290.498108977, 147.915909522, -0.0322922289089
4given(0.309894876076, -0.950770822119, 9.79208863217E-5), (0.950770827162, 0.309894874482, -3.14380126223E-5), (-4.54835669087E-7, 0.00010284280111, 0.999999994712)198.870518996, -31.5673190571, -0.0186155039026

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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


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


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

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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

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: 105.98 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002816455
ELECTRON MICROSCOPYf_angle_d0.511422490
ELECTRON MICROSCOPYf_chiral_restr0.03962620
ELECTRON MICROSCOPYf_plane_restr0.00432760
ELECTRON MICROSCOPYf_dihedral_angle_d10.77815795
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints3.36679774791E-13
ens_1d_3AAELECTRON MICROSCOPYNCS constraints2.39092598976E-12
ens_1d_4AAELECTRON MICROSCOPYNCS constraints2.07149530198E-10
ens_1d_5AAELECTRON MICROSCOPYNCS constraints6.28913111991E-13

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