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- PDB-8a5u: Crystal structure of the beta3 subunit extracellular domain of ni... -

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Basic information

Entry
Database: PDB / ID: 8a5u
TitleCrystal structure of the beta3 subunit extracellular domain of nicotinic acetylcholine receptor
ComponentsNeuronal acetylcholine receptor subunit beta-3
KeywordsMEMBRANE PROTEIN / beta3 nicotinic acetylcholine receptor / pentameric receptors / ligand gated ion channels
Function / homology
Function and homology information


Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / dopaminergic synapse / excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic transmission, cholinergic / acetylcholine binding / nervous system process / anchoring junction / channel activity ...Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine-gated channel complex / dopaminergic synapse / excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic transmission, cholinergic / acetylcholine binding / nervous system process / anchoring junction / channel activity / acetylcholine-gated monoatomic cation-selective channel activity / neurotransmitter receptor activity / regulation of synaptic vesicle exocytosis / heterocyclic compound binding / plasma membrane => GO:0005886 / monoatomic ion transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / response to nicotine / transmembrane signaling receptor activity / chemical synaptic transmission / postsynaptic membrane / membrane => GO:0016020 / neuron projection / synapse / signal transduction / 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 / 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
Neuronal acetylcholine receptor subunit beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGiastas, P. / Zouridakis, M.
Funding support Greece, 1items
OrganizationGrant numberCountry
Hellenic Foundation for Research and Innovation (HFRI)677 Greece
CitationJournal: Molecules / Year: 2022
Title: Structural Insights into the Role of beta 3 nAChR Subunit in the Activation of Nicotinic Receptors.
Authors: Giastas, P. / Papakyriakou, A. / Tsafaras, G. / Tzartos, S.J. / Zouridakis, M.
History
DepositionJun 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Neuronal acetylcholine receptor subunit beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6755
Polymers26,0071
Non-polymers6684
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.998, 66.772, 73.591
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Neuronal acetylcholine receptor subunit beta-3


Mass: 26007.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNB3 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q05901
#2: 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.: 2 / 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
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 10% w/v PEG 6000, 100 mM Bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→49.45 Å / Num. obs: 10319 / % possible obs: 99.86 % / Redundancy: 6 % / Biso Wilson estimate: 50.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.021 / Net I/σ(I): 16.33
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.24 / Num. unique obs: 1020 / CC1/2: 0.9 / % possible all: 99.51

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uxu

4uxu


Resolution: 2.4→49.45 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2816 458 4.44 %
Rwork0.211 9850 -
obs0.2137 10308 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.67 Å2 / Biso mean: 63.4374 Å2 / Biso min: 31.35 Å2
Refinement stepCycle: final / Resolution: 2.4→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 61 49 1758
Biso mean--76.81 56.09 -
Num. residues----201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.750.33011440.265532113355
2.75-3.460.28221640.245832333397
3.46-49.450.27091500.187734063556
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9521-0.1413-0.11052.46171.5551.7879-0.1098-0.2185-0.1003-0.1213-0.01970.29240.14350.0271-0.0150.27210.04780.00190.41280.03910.408512.6624-0.391822.2755
20.59390.5978-0.34270.5890.04540.5883-0.1973-0.22770.0895-0.3562-0.13750.14690.0728-0.1222-0.00120.37540.0914-0.10610.4215-0.08270.42710.37324.587116.8999
31.2460.45720.91872.7636-0.36890.7712-0.07620.08490.2387-0.4508-0.07210.1349-0.59830.3023-0.00040.50320.0259-0.03140.3071-0.01290.328114.875520.048913.6033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 93 )B1 - 93
2X-RAY DIFFRACTION2chain 'B' and (resid 94 through 128 )B94 - 128
3X-RAY DIFFRACTION3chain 'B' and (resid 129 through 207 )B129 - 207

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