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- PDB-4zjs: Crystal structure of a chimeric acetylcholine binding protein fro... -

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Basic information

Entry
Database: PDB / ID: 4zjs
TitleCrystal structure of a chimeric acetylcholine binding protein from Aplysia Californica (Ac-AChBP) containing the main immunogenic region (MIR) from the human alpha 1 subunit of the muscle nicotinic acetylcholine receptor in complex with anatoxin-A.
ComponentsAcetylcholine receptor subunit alpha,Soluble acetylcholine receptor,Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor
KeywordsIMMUNE SYSTEM / anatoxin-A / nicotinic / receptor / acetylcholine
Function / homology
Function and homology information


skeletal muscle tissue growth / musculoskeletal movement / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / neuromuscular synaptic transmission / acetylcholine-gated monoatomic cation-selective channel activity / acetylcholine binding / synaptic transmission, cholinergic ...skeletal muscle tissue growth / musculoskeletal movement / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / acetylcholine-gated channel complex / neuromuscular synaptic transmission / acetylcholine-gated monoatomic cation-selective channel activity / acetylcholine binding / synaptic transmission, cholinergic / acetylcholine receptor signaling pathway / postsynaptic specialization membrane / neuromuscular process / muscle cell cellular homeostasis / neuromuscular junction development / membrane depolarization / skeletal muscle contraction / neuronal action potential / extracellular ligand-gated monoatomic ion channel activity / response to nicotine / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / neuromuscular junction / neuron cellular homeostasis / transmembrane signaling receptor activity / monoatomic ion transmembrane transport / postsynaptic membrane / neuron projection / synapse / cell surface / metal ion binding / identical protein binding / 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
Chem-4P0 / Acetylcholine receptor subunit alpha / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Aplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2301 Å
AuthorsTalley, T.T. / Bobango, J. / Wu, J. / Park, J.F. / Luo, J. / Lindsatrom, J. / Taylor, P.
CitationJournal: J. Neurosci. / Year: 2009
Title: Main immunogenic region structure promotes binding of conformation-dependent myasthenia gravis autoantibodies, nicotinic acetylcholine receptor conformation maturation, and agonist sensitivity.
Authors: Luo, J. / Taylor, P. / Losen, M. / de Baets, M.H. / Shelton, G.D. / Lindstrom, J.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor,Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor
B: Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor,Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor
C: Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor,Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor
D: Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor,Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor
E: Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor,Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,0428
Polymers131,5465
Non-polymers4963
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12720 Å2
ΔGint-63 kcal/mol
Surface area40820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.604, 207.604, 207.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor,Acetylcholine receptor subunit alpha,Soluble acetylcholine receptor


Mass: 26309.240 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aplysia californica (California sea hare)
Gene: CHRNA1, ACHRA, CHNRA / Production host: Homo sapiens (human) / References: UniProt: P02708, UniProt: Q8WSF8
#2: Chemical ChemComp-4P0 / 1-[(1R,6R)-9-azabicyclo[4.2.1]non-2-en-2-yl]ethanone


Mass: 165.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop
Details: 17. 25.5% PEG 4000, 0.085 M Tris HCl pH 8.5, 0.17 M Lithium Sulfate, 15% Glycerol
PH range: 8.5

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Data collection

DiffractionMean temperature: 88 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. all: 72166 / Num. obs: 72156 / % possible obs: 100 % / Redundancy: 37.9 % / Biso Wilson estimate: 36.57 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 5
Reflection shellResolution: 2.23→2.27 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.952 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BYN, 2PGZ, 2BYP, 2BYS, 2BYR, 3C84, and a homology model

2byn

2pgz

2byp

2bys

2byr

3c84


Resolution: 2.2301→48.93 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 1999 2.78 %
Rwork0.197 --
obs0.197 71956 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2301→48.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8044 0 36 181 8261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078306
X-RAY DIFFRACTIONf_angle_d1.03411364
X-RAY DIFFRACTIONf_dihedral_angle_d13.2782890
X-RAY DIFFRACTIONf_chiral_restr0.041301
X-RAY DIFFRACTIONf_plane_restr0.0041459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2301-2.28590.26411420.22674975X-RAY DIFFRACTION100
2.2859-2.34770.29411420.22154987X-RAY DIFFRACTION100
2.3477-2.41680.27121420.21544977X-RAY DIFFRACTION100
2.4168-2.49480.23291480.20985022X-RAY DIFFRACTION100
2.4948-2.58390.27451410.22874915X-RAY DIFFRACTION100
2.5839-2.68740.26861410.2344979X-RAY DIFFRACTION100
2.6874-2.80970.29331440.22974944X-RAY DIFFRACTION99
2.8097-2.95780.31761390.23844943X-RAY DIFFRACTION99
2.9578-3.14310.32371430.22714976X-RAY DIFFRACTION99
3.1431-3.38570.23531390.21674986X-RAY DIFFRACTION100
3.3857-3.72630.20481410.19565011X-RAY DIFFRACTION100
3.7263-4.26520.2031440.16585027X-RAY DIFFRACTION100
4.2652-5.37270.1771460.15265046X-RAY DIFFRACTION100
5.3727-48.94450.17771470.18225169X-RAY DIFFRACTION100

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