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

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Basic information

Entry
Database: PDB / ID: 7ekt
Titlehuman alpha 7 nicotinic acetylcholine receptor bound to EVP-6124 and PNU-120596
ComponentsNeuronal acetylcholine receptor subunit alpha-7
KeywordsMEMBRANE PROTEIN / alpha 7 / nicotinic acetylcholine receptor / agonist / PAM
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 / Chem-I33 / Chem-I34 / Neuronal acetylcholine receptor subunit alpha-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 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 1.2Nov 20, 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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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)290,85030
Polymers282,5265
Non-polymers8,32425
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_1I33I33M
d_14ens_1I34I34N
d_15ens_1NAGNAGF
d_16ens_1NAGNAGF
d_17ens_1NAGNAGK
d_18ens_1CLRCLRL
d_21ens_1GLYGLYB1 - 114
d_22ens_1CYSALAB116 - 396
d_23ens_1I33I33O
d_24ens_1I34I34P
d_25ens_1NAGNAGG
d_26ens_1NAGNAGG
d_27ens_1NAGNAGQ
d_28ens_1CLRCLRR
d_31ens_1GLYGLYC1 - 114
d_32ens_1CYSALAC116 - 396
d_33ens_1I33I33S
d_34ens_1I34I34T
d_35ens_1NAGNAGH
d_36ens_1NAGNAGH
d_37ens_1NAGNAGU
d_38ens_1CLRCLRV
d_41ens_1GLYGLYD1 - 114
d_42ens_1CYSALAD116 - 396
d_43ens_1I33I33W
d_44ens_1I34I34X
d_45ens_1NAGNAGI
d_46ens_1NAGNAGI
d_47ens_1NAGNAGY
d_48ens_1CLRCLRZ
d_51ens_1GLYGLYE1 - 114
d_52ens_1CYSALAE116 - 396
d_53ens_1I33I33AA
d_54ens_1I34I34BA
d_55ens_1NAGNAGJ
d_56ens_1NAGNAGJ
d_57ens_1NAGNAGCA
d_58ens_1CLRCLRDA

NCS oper:
IDCodeMatrixVector
1given(0.307606541786, -0.951513433975, 0.000632784120891), (0.951513639264, 0.307606403112, -0.000308317288429), (9.87195944938E-5, 0.000696943136604, 0.999999752262)199.9871394, -31.4531822951, -0.140004511822
2given(-0.809801808111, -0.586703192125, 0.000629230109493), (0.58670349574, -0.809801659798, 0.000529031616343), (0.000199167049019, 0.000797582264327, 0.999999662097)291.513986066, 148.794983646, -0.158325980636
3given(-0.808415300426, 0.588612517977, -7.56179662622E-5), (-0.588612490339, -0.808415206435, 0.000436144195689), (0.00019558921942, 0.000397095320423, 0.99999990203)148.388092839, 291.644250495, -0.0884314058769
4given(0.31010349826, 0.950702749497, -0.000320102622106), (-0.950702798014, 0.310103514726, 1.90233134549E-6), (0.000101073499829, 0.000303732538882, 0.999999948765)-31.7164452761, 199.580620021, -0.0587667708726

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Components

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Protein , 1 types, 5 molecules ABCDE

#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

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Sugars , 2 types, 10 molecules

#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-Glycam 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
[]{[(4+1)][b-D-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

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Non-polymers , 3 types, 15 molecules

#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H46O
#5: 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
#6: Chemical
ChemComp-I34 / N-(5-Chloro-2,4-dimethoxyphenyl)-N'-(5-methyl-3-isoxazolyl)-urea


Mass: 311.721 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H14ClN3O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

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 EVP-6124 and PNU-120596
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
NameVersionClassificationNB
phenix.real_space_refine1.19_4092refinement
PHENIX1.19_4092refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46899 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 87.57 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002716665
ELECTRON MICROSCOPYf_angle_d0.589822795
ELECTRON MICROSCOPYf_chiral_restr0.04722635
ELECTRON MICROSCOPYf_plane_restr0.00422780
ELECTRON MICROSCOPYf_dihedral_angle_d11.25045845
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.000597027403305
ens_1d_3AELECTRON MICROSCOPYNCS constraints0.000616055031402
ens_1d_4AELECTRON MICROSCOPYNCS constraints0.000686480994244
ens_1d_5AELECTRON MICROSCOPYNCS constraints0.000855280558509

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