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- PDB-4uxu: Crystal Structure of the Extracellular Domain of the Human Alpha9... -

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Entry
Database: PDB / ID: 4uxu
TitleCrystal Structure of the Extracellular Domain of the Human Alpha9 Nicotinic Acetylcholine Receptor In Complex with Methyllycaconitine
ComponentsNEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9
KeywordsTRANSPORT PROTEIN / TRANSPORT / NEURONAL TYPE NACHR / EXTRACELLULAR DOMAIN / METHYLLYCACONITINE / ANTAGONIST
Function / homology
Function and homology information


Acetylcholine inhibits contraction of outer hair cells / serotonin-gated monoatomic cation channel activity / cholinergic synapse / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex / response to auditory stimulus / detection of mechanical stimulus involved in sensory perception of sound / acetylcholine-gated monoatomic cation-selective channel activity / transmembrane transporter complex ...Acetylcholine inhibits contraction of outer hair cells / serotonin-gated monoatomic cation channel activity / cholinergic synapse / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex / response to auditory stimulus / detection of mechanical stimulus involved in sensory perception of sound / acetylcholine-gated monoatomic cation-selective channel activity / transmembrane transporter complex / inner ear morphogenesis / postsynaptic specialization membrane / membrane depolarization / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / negative regulation of ERK1 and ERK2 cascade / calcium channel activity / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / chemical synaptic transmission / neuron projection / synapse / 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
METHYLLYCACONITINE / Neuronal acetylcholine receptor subunit alpha-9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsZouridakis, M. / Giastas, P. / Zarkadas, E. / Tzartos, S.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Crystal Structures of Free and Antagonist-Bound States of Human Alpha9 Nicotinic Receptor Extracellular Domain
Authors: Zouridakis, M. / Giastas, P. / Zarkadas, E. / Chroni-Tzartou, D. / Bregestovski, P. / Tzartos, S.J.
History
DepositionAug 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Nov 19, 2014Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9
B: NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,05017
Polymers50,6142
Non-polymers3,43615
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-5 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.434, 66.246, 75.191
Angle α, β, γ (deg.)90.00, 102.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9 / NICOTINIC ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9 / NACHR ALP HA-9 / HUMAN ALPHA9 NICOTINIC ...NICOTINIC ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9 / NACHR ALP HA-9 / HUMAN ALPHA9 NICOTINIC ACETYLCHOLINE RECEPTOR


Mass: 25307.029 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 26-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZAA / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X33 / References: UniProt: Q9UGM1
#6: 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.: 4
Source method: isolated from a genetically manipulated source
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 , 5 types, 513 molecules

#2: Chemical ChemComp-MLK / METHYLLYCACONITINE


Mass: 682.800 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H50N2O10 / Comment: alkaloid*YM
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsEXTRACELLULAR DOMAIN

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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: 3.1 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M HEPES PH 7.5, 15% PEG 20000, 7.5% ETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→41.6 Å / Num. obs: 63697 / % possible obs: 97.9 % / Observed criterion σ(I): 1.4 / Redundancy: 3.5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 1.4 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D01

4d01


Resolution: 1.71→41.606 Å / SU ML: 0.22 / σ(F): 1.33 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 3232 5.1 %
Rwork0.206 --
obs0.2112 63592 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.3 Å2
Refinement stepCycle: LAST / Resolution: 1.71→41.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 228 502 4146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073775
X-RAY DIFFRACTIONf_angle_d1.3445197
X-RAY DIFFRACTIONf_dihedral_angle_d16.8981410
X-RAY DIFFRACTIONf_chiral_restr0.059586
X-RAY DIFFRACTIONf_plane_restr0.005653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.73550.31751260.29272510X-RAY DIFFRACTION93
1.7355-1.76260.33071430.28192544X-RAY DIFFRACTION94
1.7626-1.79150.30761430.2762549X-RAY DIFFRACTION94
1.7915-1.82240.3411200.27232574X-RAY DIFFRACTION95
1.8224-1.85560.29331380.25362589X-RAY DIFFRACTION96
1.8556-1.89130.2711370.24592622X-RAY DIFFRACTION97
1.8913-1.92990.30461250.24522665X-RAY DIFFRACTION98
1.9299-1.97180.28311410.23712628X-RAY DIFFRACTION98
1.9718-2.01770.26231780.22652634X-RAY DIFFRACTION98
2.0177-2.06820.26941440.22112637X-RAY DIFFRACTION98
2.0682-2.12410.27841580.21332633X-RAY DIFFRACTION97
2.1241-2.18660.2371310.21332656X-RAY DIFFRACTION98
2.1866-2.25710.24391580.21052590X-RAY DIFFRACTION98
2.2571-2.33780.27581330.22382674X-RAY DIFFRACTION97
2.3378-2.43140.25131250.22022646X-RAY DIFFRACTION98
2.4314-2.54210.23341390.22382654X-RAY DIFFRACTION97
2.5421-2.67610.23411460.21882616X-RAY DIFFRACTION97
2.6761-2.84370.28141140.21772676X-RAY DIFFRACTION98
2.8437-3.06320.22391580.21212629X-RAY DIFFRACTION97
3.0632-3.37130.19781390.19432635X-RAY DIFFRACTION96
3.3713-3.85890.19921380.18772618X-RAY DIFFRACTION95
3.8589-4.86060.17711330.17422635X-RAY DIFFRACTION96
4.8606-41.61790.22031650.18882746X-RAY DIFFRACTION98
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)
12.2604-1.3176-1.55242.00731.06792.4817-0.15480.2043-0.41210.1005-0.12330.36450.328-0.49470.27110.1932-0.0196-0.00930.2759-0.01480.2555-23.51981.10691.2594
21.16310.4806-0.48140.5047-0.06740.7492-0.0203-0.2637-0.03630.0178-0.0454-0.0450.00330.0360.06270.2170.0138-0.01390.1793-0.01350.20464.10818.0765-1.3864
31.5637-0.4662-0.60990.57490.14060.9383-0.11920.1776-0.0789-0.1099-0.00920.20060.0163-0.18140.1260.20860.0109-0.03010.2195-0.02460.2209-19.53887.18480.6708
42.3426-1.3734-1.22970.83490.74080.7237-0.4552-0.68570.12270.44770.3419-0.04890.5720.1940.01910.37710.0638-0.01030.3319-0.00310.23993.9552-0.02645.7192
51.3695-0.1721-0.10310.39790.16440.7818-0.0338-0.15890.1330.0354-0.03440.0099-0.0099-0.14890.06940.17120.0127-0.00090.15290.00390.1691-8.39698.64940.2349
60.67050.6151-0.00880.9178-0.1920.2823-0.0361-0.0156-0.1249-0.0902-0.0441-0.11680.0390.04140.08790.25970.02350.02740.1832-0.00890.17147.90243.1138-10.0417
70.87250.2087-0.03570.78130.25970.9322-0.0093-0.04590.0488-0.0514-0.0104-0.07940.00590.0670.05720.24960.00850.01060.13880.00540.15767.68597.7628-9.5755
80.70760.61391.39221.60541.20893.2571-0.11770.04310.1621-0.135-0.16130.1877-0.455-0.57910.31090.21390.011-0.00650.3017-0.03050.2423-12.409-7.5669-47.9673
91.3498-0.53540.49810.5789-0.35751.0695-0.0790.1243-0.07130.0375-0.0215-0.0518-0.06270.13590.10210.2809-0.01540.0270.1731-0.01220.182211.397-14.5736-33.6619
101.44430.72470.42850.99660.48861.6828-0.1182-0.0489-0.0849-0.0872-0.09910.1442-0.0253-0.33030.19220.2444-0.01510.0140.2309-0.03850.2223-9.1172-13.6458-45.7349
111.79871.45691.69911.18571.3781.601-0.14810.5579-0.2091-0.52840.4336-0.236-0.75470.4793-0.27810.4452-0.07160.02370.2922-0.02570.25514.0129-6.5305-40.333
121.92120.20810.40820.53340.33531.10150.09170.1781-0.19750.0287-0.09640.00790.0577-0.0906-0.02210.2808-0.01490.0160.171-0.01480.17920.752-15.0759-40.2714
130.514-0.51040.05880.7596-0.2860.5243-0.0614-0.00810.0260.1013-0.0199-0.0753-0.1010.06560.08440.3099-0.01510.00730.193-0.00440.18111.1239-9.5989-24.202
140.8213-0.2486-0.06560.930.42180.48-0.00880.0373-0.07510.03890.0033-0.0247-0.04220.08660.02860.3373-0.00550.02710.16060.00480.151611.1201-14.2732-24.6816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 30 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 31 THROUGH 63 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 64 THROUGH 94 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 95 THROUGH 108 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 109 THROUGH 129 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 130 THROUGH 162 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 163 THROUGH 212 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 3 THROUGH 30 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 31 THROUGH 63 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 64 THROUGH 94 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 95 THROUGH 108 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 109 THROUGH 129 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 130 THROUGH 162 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 163 THROUGH 212 )

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