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- PDB-4zk4: Crystal structure of a chimeric acetylcholine binding protein fro... -

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Basic information

Entry
Database: PDB / ID: 4zk4
TitleCrystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane
Componentssoluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera
KeywordsACETYLCHOLINE BINDING PROTEIN / AChBP / nicotinic / receptor / acetylcholine
Function / homology
Function and homology information


regulation of acetylcholine secretion, neurotransmission / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / regulation of smooth muscle contraction / behavioral response to nicotine ...regulation of acetylcholine secretion, neurotransmission / synaptic transmission involved in micturition / Highly sodium permeable postsynaptic acetylcholine nicotinic receptors / Highly calcium permeable nicotinic acetylcholine receptors / Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / acetylcholine receptor activity / response to acetylcholine / acetylcholine-gated channel complex / regulation of smooth muscle contraction / behavioral response to nicotine / acetylcholine-gated monoatomic cation-selective channel activity / acetylcholine binding / synaptic transmission, cholinergic / acetylcholine receptor signaling pathway / activation of transmembrane receptor protein tyrosine kinase activity / excitatory extracellular ligand-gated monoatomic ion channel activity / regulation of dendrite morphogenesis / plasma membrane raft / membrane depolarization / ligand-gated monoatomic ion channel activity / monoatomic ion transport / regulation of membrane potential / excitatory postsynaptic potential / response to nicotine / locomotory behavior / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / nervous system development / postsynaptic membrane / postsynapse / postsynaptic density / nuclear speck / neuron projection / neuronal cell body / dendrite / synapse / Golgi apparatus / endoplasmic reticulum / signal transduction / identical protein binding / membrane / metal ion binding / 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-TII / Neuronal acetylcholine receptor subunit alpha-3 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsBobango, J. / Wu, J. / Talley, T.T.
CitationJournal: To be Published
Title: Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with 7-(5- ...Title: Crystal structure of a chimeric acetylcholine binding protein from Aplysia californica (Ac-AChBP) containing loop C from the human alpha 3 nicotinic acetylcholine receptor in complex with 7-(5-isopropoxy-pyridin-3-yl)-1-methyl-1,7-diaza-spiro[4.4]nonane.
Authors: Bobango, J. / Wu, J. / Talley, T.T.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
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_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_keywords
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_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_keywords.text
Revision 1.2Oct 16, 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: soluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera
B: soluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera
C: soluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera
D: soluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera
E: soluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,27515
Polymers131,0015
Non-polymers1,27410
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-118 kcal/mol
Surface area41960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.662, 78.205, 120.465
Angle α, β, γ (deg.)90.000, 94.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
soluble acetylcholine receptor, neuronal acetylcholine receptor subunit alpha-3 chimera


Mass: 26200.197 Da / Num. of mol.: 5
Fragment: UNP residues 18-198 + 215-236 from Aplysia californica linked by loop C (UNP residues 215-230) from Homo sapiens
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare), (gene. exp.) Homo sapiens (human)
Gene: CHRNA3, NACHRA3 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8, UniProt: P32297

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Non-polymers , 5 types, 449 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-TII / (5R)-1-methyl-7-[5-(propan-2-yloxy)pyridin-3-yl]-1,7-diazaspiro[4.4]nonane


Mass: 275.389 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N3O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.7% PEG400, 0.085 M HEPES sodium, pH 7.5, 1.7 M ammonium sulfate, 15% glycerol

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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: Dec 20, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 110948 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.09 Å2 / Rmerge(I) obs: 0.086 / Χ2: 2.82 / Net I/av σ(I): 40.746 / Net I/σ(I): 13.9 / Num. measured all: 812969
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.8850.58452941.03995.9
1.88-1.9260.52254951.00698.9
1.92-1.957.20.44255081.006100
1.95-1.997.50.38655511.08100
1.99-2.047.50.30855101.049100
2.04-2.087.50.26455131.106100
2.08-2.147.60.22855651.228100
2.14-2.197.60.19955591.32100
2.19-2.267.60.18255111.385100
2.26-2.337.60.15855361.543100
2.33-2.417.60.13755671.692100
2.41-2.517.60.1355891.826100
2.51-2.637.60.11455292.094100
2.63-2.767.60.10355422.548100
2.76-2.947.60.09656073.424100
2.94-3.167.60.08855494.782100
3.16-3.487.60.07955576.581100
3.48-3.997.50.07156017.483100
3.99-5.027.40.05656396.809100
5.02-507.40.04457266.04599.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2BYN, 2BYP, 2BYR, 2BYS, 2PGZ, 3C79, 3C84

2byn

2byp

2byr

2bys

2pgz

3c79

3c84


Resolution: 1.901→49.135 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 21.85 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2125 5132 5 %
Rwork0.1811 97506 -
obs0.1826 102638 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.51 Å2 / Biso mean: 32.2759 Å2 / Biso min: 11.78 Å2
Refinement stepCycle: final / Resolution: 1.901→49.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7974 0 148 439 8561
Biso mean--43.72 31.94 -
Num. residues----1034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0148269
X-RAY DIFFRACTIONf_angle_d1.31811315
X-RAY DIFFRACTIONf_chiral_restr0.0521288
X-RAY DIFFRACTIONf_plane_restr0.0061443
X-RAY DIFFRACTIONf_dihedral_angle_d14.5412842
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9013-1.92290.26541620.21013092325496
1.9229-1.94550.26231880.197432393427100
1.9455-1.96920.26441590.190932273386100
1.9692-1.99420.24131740.192232443418100
1.9942-2.02040.23651500.187532693419100
2.0204-2.04810.22341570.17531993356100
2.0481-2.07730.22761560.181433113467100
2.0773-2.10830.2251560.182432393395100
2.1083-2.14130.22281700.181232233393100
2.1413-2.17640.2211780.180632123390100
2.1764-2.21390.24231640.176232583422100
2.2139-2.25420.21231840.181132173401100
2.2542-2.29750.2111540.18232793433100
2.2975-2.34440.22521790.187432423421100
2.3444-2.39540.2311850.173632363421100
2.3954-2.45110.19571620.178232913453100
2.4511-2.51240.22891820.185332243406100
2.5124-2.58040.21212040.19231793383100
2.5804-2.65630.23171920.188932213413100
2.6563-2.7420.24191660.195232833449100
2.742-2.840.21931650.199132533418100
2.84-2.95370.26912000.199332323432100
2.9537-3.08810.25191770.206732573434100
3.0881-3.25090.24431720.198132573429100
3.2509-3.45450.21991730.187132623435100
3.4545-3.72120.21921550.180933243479100
3.7212-4.09550.18431700.165132593429100
4.0955-4.68770.15181480.146432923440100
4.6877-5.90440.17111760.155633163492100
5.9044-49.15190.18531740.195733693543100

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