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- PDB-5kxi: X-ray structure of the human Alpha4Beta2 nicotinic receptor -

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Basic information

Entry
Database: PDB / ID: 5kxi
TitleX-ray structure of the human Alpha4Beta2 nicotinic receptor
Components(Neuronal acetylcholine receptor subunit ...) x 2
KeywordsTRANSPORT PROTEIN / acetylcholine receptor / Cys-loop receptor / ligand-gated ion channel / membrane protein
Function / homology
Function and homology information


vestibulocochlear nerve development / lateral geniculate nucleus development / regulation of circadian sleep/wake cycle, REM sleep / regulation of synaptic transmission, dopaminergic / quaternary ammonium group binding / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / optic nerve morphogenesis / response to acetylcholine ...vestibulocochlear nerve development / lateral geniculate nucleus development / regulation of circadian sleep/wake cycle, REM sleep / regulation of synaptic transmission, dopaminergic / quaternary ammonium group binding / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / optic nerve morphogenesis / response to acetylcholine / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / central nervous system projection neuron axonogenesis / acetylcholine-gated channel complex / cholinergic synapse / regulation of dopamine metabolic process / negative regulation of action potential / behavioral response to nicotine / positive regulation of dopamine secretion / acetylcholine receptor activity / inhibitory postsynaptic potential / synaptic transmission, cholinergic / acetylcholine binding / postsynaptic specialization membrane / nervous system process / acetylcholine receptor signaling pathway / acetylcholine-gated monoatomic cation-selective channel activity / regulation of synapse assembly / action potential / regulation of dendrite morphogenesis / heterocyclic compound binding / B cell activation / regulation of dopamine secretion / plasma membrane raft / membrane depolarization / associative learning / social behavior / ligand-gated monoatomic ion channel activity / smooth muscle contraction / monoatomic ion transport / positive regulation of B cell proliferation / sensory perception of pain / visual perception / response to cocaine / learning / locomotory behavior / regulation of membrane potential / sensory perception of sound / response to nicotine / visual learning / memory / cognition / calcium ion transport / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / response to ethanol / response to oxidative stress / response to hypoxia / neuron projection / external side of plasma membrane / DNA repair / neuronal cell body / synapse / dendrite / protein-containing complex binding / signal transduction / 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
(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / Neuronal acetylcholine receptor subunit beta-2 / Neuronal acetylcholine receptor subunit alpha-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.941 Å
AuthorsMorales-Perez, C.L. / Noviello, C.M. / Hibbs, R.E.
Funding support United States, 9items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)T32 NS069562 United States
Howard Hughes Medical Institute (HHMI)Gilliam Fellowship United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA037492 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS077983 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS095899 United States
Welch FoundationI-1812 United States
McKnight Scholar Award United States
Klingenstein-Simons Fellowship Award United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA042072 United States
CitationJournal: Nature / Year: 2016
Title: X-ray structure of the human alpha 4 beta 2 nicotinic receptor.
Authors: Morales-Perez, C.L. / Noviello, C.M. / Hibbs, R.E.
History
DepositionJul 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuronal acetylcholine receptor subunit alpha-4
B: Neuronal acetylcholine receptor subunit beta-2
C: Neuronal acetylcholine receptor subunit beta-2
D: Neuronal acetylcholine receptor subunit alpha-4
E: Neuronal acetylcholine receptor subunit beta-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,42513
Polymers229,9715
Non-polymers1,4538
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28830 Å2
ΔGint-178 kcal/mol
Surface area74570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.099, 132.633, 202.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Neuronal acetylcholine receptor subunit ... , 2 types, 5 molecules ADBCE

#1: Protein Neuronal acetylcholine receptor subunit alpha-4


Mass: 44862.367 Da / Num. of mol.: 2
Fragment: UNP residues 27-364, 586-627,UNP residues 27-364, 586-627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNA4, NACRA4 / Production host: Homo sapiens (human) / References: UniProt: P43681
#2: Protein Neuronal acetylcholine receptor subunit beta-2


Mass: 46748.863 Da / Num. of mol.: 3
Fragment: UNP residues 26-355,446-502,UNP residues 26-353,446-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHRNB2 / Production host: Homo sapiens (human) / References: UniProt: P17787

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Sugars , 1 types, 5 molecules

#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, 8 molecules

#4: Chemical ChemComp-NCT / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / (S)-(-)-NICOTINE / 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE


Mass: 162.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H14N2 / Comment: alkaloid*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 0.05 M ADA pH 6.8, 12.5% PEG 1500 and 10% PEG 1000

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.94→40 Å / Num. obs: 30759 / % possible obs: 99.5 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.044 / Net I/σ(I): 14.9
Reflection shellResolution: 3.94→4.01 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.547 / Rpim(I) all: 0.716 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model

Resolution: 3.941→24.996 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.78
RfactorNum. reflection% reflection
Rfree0.3074 1330 4.98 %
Rwork0.2849 --
obs0.286 26718 86.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.941→24.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14705 0 95 5 14805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315223
X-RAY DIFFRACTIONf_angle_d0.74520807
X-RAY DIFFRACTIONf_dihedral_angle_d18.2885519
X-RAY DIFFRACTIONf_chiral_restr0.0452448
X-RAY DIFFRACTIONf_plane_restr0.0062533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9407-4.08090.4016500.3761953X-RAY DIFFRACTION33
4.0809-4.24360.3672970.36951671X-RAY DIFFRACTION59
4.2436-4.43570.29571260.33392286X-RAY DIFFRACTION79
4.4357-4.66810.34031380.30472798X-RAY DIFFRACTION97
4.6681-4.95850.37211490.3032899X-RAY DIFFRACTION99
4.9585-5.33790.31931550.29292910X-RAY DIFFRACTION100
5.3379-5.86870.29751720.29412884X-RAY DIFFRACTION100
5.8687-6.70360.33471300.32582956X-RAY DIFFRACTION100
6.7036-8.39240.29921550.27962965X-RAY DIFFRACTION100
8.3924-24.99670.2771580.253066X-RAY DIFFRACTION99
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)
17.98813.1543-5.0973.0757-2.52575.04150.2422-0.2235-1.12550.3402-0.2927-0.8997-0.28470.125401.66540.1753-0.05361.4226-0.03781.88373.777-19.0905-26.902
25.63280.73983.75271.8199-1.38970.49030.7795-2.497-1.8070.433-0.0251.48030.093-0.7206-01.6158-0.02060.26972.73470.58462.190118.9977-20.5078-5.8247
310.8137-0.3129-3.15841.9489-0.27214.3989-0.12980.0741-0.0737-1.0761-0.2724-0.45040.29670.039501.94440.1570.10081.2421-0.00881.433161.104-20.9502-50.1244
42.31120.89430.7442.57561.30141.2409-0.3382-0.0549-0.41310.20960.06341.30240.2667-1.090501.53590.1090.19972.42660.24442.16099.834-13.0864-24.6448
57.68691.3892-5.51073.71110.41796.83650.08040.35520.11720.0555-0.3181-0.7725-0.5436-0.074801.8478-0.0220.21291.2407-0.161.917165.545721.5556-40.3198
61.8461-1.6315-2.49232.76133.83811.84590.3405-0.494-0.30550.7789-0.34710.3894-1.2652-0.9549-02.44770.7320.51842.65520.09611.909419.437115.7746-3.9826
78.93860.5531-2.82534.05270.74654.9127-0.06010.1591-0.0438-1.05410.5269-0.4829-0.1075-0.0163-01.93380.04580.03771.25960.05631.350155.74174.0283-58.6736
80.2169-2.33170.5874.85951.57983.2277-0.0390.1066-0.55850.53350.04911.6685-0.6863-1.803701.42080.35920.1142.6222-0.01562.02539.81399.5629-23.9046
95.48820.954-2.18142.8896-1.49554.3469-0.1934-0.2996-0.25120.1885-0.1921-1.0719-0.17680.365101.6361-0.0382-0.34571.5918-0.26862.026377.74637.7345-21.1054
102.15480.66760.8164-1.16283.64446.14720.9156-1.5166-0.2880.8719-0.5311-0.080.2367-1.520402.19520.15870.15092.4120.13761.934927.3576-2.41885.734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 381 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 206 )
4X-RAY DIFFRACTION4chain 'B' and (resid 207 through 373 )
5X-RAY DIFFRACTION5chain 'D' and (resid 8 through 217 )
6X-RAY DIFFRACTION6chain 'D' and (resid 218 through 381 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 206 )
8X-RAY DIFFRACTION8chain 'C' and (resid 207 through 373 )
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 206 )
10X-RAY DIFFRACTION10chain 'E' and (resid 207 through 373 )

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