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- PDB-7ekp: human alpha 7 nicotinic acetylcholine receptor bound to EVP-6124 -

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Basic information

Entry
Database: PDB / ID: 7ekp
Titlehuman alpha 7 nicotinic acetylcholine receptor bound to EVP-6124
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 receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / acetylcholine-gated monoatomic cation-selective channel activity / cation channel complex ...sensory processing / dendrite arborization / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / regulation of amyloid fibril formation / short-term memory / acetylcholine-gated monoatomic cation-selective channel activity / cation channel complex / dendritic spine organization / acetylcholine binding / chloride channel regulator activity / regulation of amyloid precursor protein catabolic process / acetylcholine receptor signaling pathway / neurotransmitter receptor complex / positive regulation of amyloid-beta formation / negative regulation of amyloid-beta formation / modulation of excitatory postsynaptic potential / response to amyloid-beta / monoatomic ion channel activity / positive regulation of protein metabolic process / negative regulation of tumor necrosis factor production / plasma membrane raft / 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 / regulation of membrane potential / excitatory postsynaptic potential / response to nicotine / synapse organization / calcium channel activity / memory / cognition / intracellular calcium ion homeostasis / positive regulation of angiogenesis / 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 / positive regulation of MAPK cascade / neuron projection / positive regulation of cell population proliferation / synapse / dendrite / 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 / Chem-I33 / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 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 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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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)289,29125
Polymers282,5265
Non-polymers6,76620
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
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 - 396
d_13ens_1I33I33K
d_14ens_1NAGNAGF
d_15ens_1NAGNAGF
d_16ens_1NAGNAGL
d_17ens_1CLRCLRM
d_21ens_1GLYGLYB1 - 114
d_22ens_1CYSALAB116 - 396
d_23ens_1I33I33N
d_24ens_1NAGNAGG
d_25ens_1NAGNAGG
d_26ens_1NAGNAGO
d_27ens_1CLRCLRP
d_31ens_1GLYGLYC1 - 114
d_32ens_1CYSALAC116 - 396
d_33ens_1I33I33Q
d_34ens_1NAGNAGH
d_35ens_1NAGNAGH
d_36ens_1NAGNAGR
d_37ens_1CLRCLRS
d_41ens_1GLYGLYD1 - 114
d_42ens_1CYSALAD116 - 396
d_43ens_1I33I33T
d_44ens_1NAGNAGI
d_45ens_1NAGNAGI
d_46ens_1NAGNAGU
d_47ens_1CLRCLRV
d_51ens_1GLYGLYE1 - 114
d_52ens_1CYSALAE116 - 396
d_53ens_1I33I33W
d_54ens_1NAGNAGJ
d_55ens_1NAGNAGJ
d_56ens_1NAGNAGX
d_57ens_1CLRCLRY

NCS oper:
IDCodeMatrixVector
1given(0.307605590359, 0.951513650448, 0.000757490332353), (-0.951513951958, 0.307605495448, 0.000241660862768), (-3.0645792774E-6, -0.000795098852066, 0.999999683904)-31.654904681, 200.045485466, 0.151737526725
2given(-0.809803949867, 0.586700191847, 0.000669079503263), (-0.58670056488, -0.809803605456, -0.00075349799573), (9.97455754279E-5, -0.00100273497567, 0.999999492287)148.747196918, 291.738172034, 0.153202173741
3given(-0.808416049684, -0.588611462462, -0.000192020605367), (0.588611460458, -0.808415851121, -0.000600227158242), (0.000198068084302, -0.000598258797142, 0.999999801428)291.734920283, 148.534278084, 0.0672758145256
4given(0.310101756489, -0.950703307238, -0.000349612192259), (0.950703350265, 0.310101806352, -9.74286297494E-5), (0.000201041092865, -0.000302164693257, 0.999999934139)199.686801164, -31.7548896661, 0.0135767297736

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


Mass: 320.837 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H17ClN2OS / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#4: 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
#5: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H46O
Has ligand of interestY
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 bound to agonist EVP-6124
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 FIELD
Image recordingElectron dose: 62 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: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59759 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 74.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002816580
ELECTRON MICROSCOPYf_angle_d0.597222670
ELECTRON MICROSCOPYf_chiral_restr0.04782635
ELECTRON MICROSCOPYf_plane_restr0.00292765
ELECTRON MICROSCOPYf_dihedral_angle_d13.0575850
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000819117201147
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000685134834802
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000551485876611
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.00066933708496

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