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- PDB-4uy2: Crystal structure of the complex of the extracellular domain of h... -

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Basic information

Entry
Database: PDB / ID: 4uy2
TitleCrystal structure of the complex of the extracellular domain of human alpha9 nAChR with alpha-bungarotoxin.
Components
  • ALPHA-BUNGAROTOXIN ISOFORM V31
  • NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9
KeywordsTOXIN-BINDING PROTEIN/TOXIN / TOXIN-BINDING PROTEIN-TOXIN COMPLEX / LIGAND BINDING DOMAIN / CYS-LOOP RECEPTOR
Function / homology
Function and homology information


Acetylcholine inhibits contraction of outer hair cells / serotonin-gated monoatomic cation channel activity / response to auditory stimulus / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / detection of mechanical stimulus involved in sensory perception of sound / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / transmembrane transporter complex ...Acetylcholine inhibits contraction of outer hair cells / serotonin-gated monoatomic cation channel activity / response to auditory stimulus / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / detection of mechanical stimulus involved in sensory perception of sound / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / transmembrane transporter complex / ion channel regulator activity / inner ear morphogenesis / membrane depolarization / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / calcium channel activity / toxin activity / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / chemical synaptic transmission / postsynaptic membrane / neuron projection / synapse / extracellular region / plasma membrane
Similarity search - Function
Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / Snake three-finger toxin / : / Snake toxin cobra-type / Nicotinic acetylcholine receptor / CD59 / CD59 / Acetylcholine Binding Protein; Chain: A, ...Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / Snake three-finger toxin / : / Snake toxin cobra-type / Nicotinic acetylcholine receptor / CD59 / CD59 / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Snake toxin-like superfamily / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Alpha-bungarotoxin isoform V31 / Neuronal acetylcholine receptor subunit alpha-9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BUNGARUS MULTICINCTUS (many-banded krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.697 Å
AuthorsGiastas, P. / Zouridakis, M. / 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 28, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
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

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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
C: ALPHA-BUNGAROTOXIN ISOFORM V31
D: ALPHA-BUNGAROTOXIN ISOFORM V31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5668
Polymers66,6814
Non-polymers8854
Water00
1
A: NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9
C: ALPHA-BUNGAROTOXIN ISOFORM V31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7834
Polymers33,3402
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint0.4 kcal/mol
Surface area15250 Å2
MethodPISA
2
B: NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9
D: ALPHA-BUNGAROTOXIN ISOFORM V31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7834
Polymers33,3402
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-0.5 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.319, 119.348, 79.107
Angle α, β, γ (deg.)90.00, 103.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NEURONAL ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9 / ALPHA9 NICOTINIC ACETYLCHOLINE RECEPTOR / NICOTINIC ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA-9 / NACHR ALPHA-9


Mass: 25307.029 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN, 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
#2: Protein ALPHA-BUNGAROTOXIN ISOFORM V31 / ALPHA-BTX V31 / ALPHA-BGT(V31) / BGTX V31 / LONG NEUROTOXIN 1


Mass: 8033.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) BUNGARUS MULTICINCTUS (many-banded krait) / References: UniProt: P60616
#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.: 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
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.8 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M MES PH 6.0, 0.2 M NACL, 30% W/V JEFFAMINE ED2003

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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: Aug 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→47 Å / Num. obs: 21021 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 67.36 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.45 / Mean I/σ(I) obs: 1 / % possible all: 97

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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 ENTRIES 1D01, 2QC1

1d01

2qc1


Resolution: 2.697→47.185 Å / SU ML: 0.54 / σ(F): 1.12 / Phase error: 46.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3312 2009 4.9 %
Rwork0.2581 --
obs0.2617 20942 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104 Å2
Refinement stepCycle: LAST / Resolution: 2.697→47.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4412 0 56 0 4468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174598
X-RAY DIFFRACTIONf_angle_d2.4256272
X-RAY DIFFRACTIONf_dihedral_angle_d18.0721656
X-RAY DIFFRACTIONf_chiral_restr0.101710
X-RAY DIFFRACTIONf_plane_restr0.014800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.697-2.76450.47821310.42762627X-RAY DIFFRACTION94
2.7645-2.83920.47871540.4122768X-RAY DIFFRACTION98
2.8392-2.92270.4661430.40772782X-RAY DIFFRACTION98
2.9227-3.01710.42271390.37672810X-RAY DIFFRACTION99
3.0171-3.12490.40951460.35162701X-RAY DIFFRACTION98
3.1249-3.250.40751440.31952843X-RAY DIFFRACTION98
3.25-3.39780.44451430.30912721X-RAY DIFFRACTION99
3.3978-3.57690.37111490.27982806X-RAY DIFFRACTION99
3.5769-3.80090.28861480.26132758X-RAY DIFFRACTION98
3.8009-4.09430.29531460.23952764X-RAY DIFFRACTION99
4.0943-4.5060.31791450.20932767X-RAY DIFFRACTION98
4.506-5.15730.251430.20322726X-RAY DIFFRACTION96
5.1573-6.4950.31971460.23642761X-RAY DIFFRACTION98
6.495-47.19180.26581320.20752792X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 13.3562 Å / Origin y: -2.5146 Å / Origin z: 7.5095 Å
111213212223313233
T0.6051 Å20.0298 Å20.002 Å2-0.433 Å20.3801 Å2--0.6552 Å2
L1.2931 °20.0146 °20.0676 °2-0.002 °20.1785 °2--2.1428 °2
S-0.0859 Å °0.3037 Å °0.0969 Å °0.0321 Å °-0.1242 Å °0.0166 Å °-0.1897 Å °0.1402 Å °0.133 Å °
Refinement TLS groupSelection details: ALL

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