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- PDB-2qc1: Crystal structure of the extracellular domain of the nicotinic ac... -

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Basic information

Entry
Database: PDB / ID: 2qc1
TitleCrystal structure of the extracellular domain of the nicotinic acetylcholine receptor 1 subunit bound to alpha-bungarotoxin at 1.9 A resolution
Components
  • Acetylcholine receptor subunit alpha
  • Alpha-bungarotoxin
KeywordsPROTEIN BINDING / nicotinic acetylcholine receptor / glycosylated protein / beta sandwich / Cys-loop / buried hydrophilic residues
Function / homology
Function and homology information


Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Highly calcium permeable nicotinic acetylcholine receptors / skeletal muscle tissue growth / musculoskeletal movement / neuromuscular synaptic transmission / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic transmission, cholinergic ...Highly calcium permeable postsynaptic nicotinic acetylcholine receptors / Highly calcium permeable nicotinic acetylcholine receptors / skeletal muscle tissue growth / musculoskeletal movement / neuromuscular synaptic transmission / excitatory extracellular ligand-gated monoatomic ion channel activity / acetylcholine-gated channel complex / acetylcholine receptor inhibitor activity / acetylcholine-gated monoatomic cation-selective channel activity / synaptic transmission, cholinergic / postsynaptic specialization membrane / ion channel regulator activity / neuromuscular process / muscle cell cellular homeostasis / neuromuscular junction development / neuronal action potential / monoatomic cation transport / skeletal muscle contraction / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to nicotine / neuromuscular junction / neuron cellular homeostasis / transmembrane signaling receptor activity / toxin activity / neuron projection / synapse / cell surface / extracellular region / membrane / plasma membrane
Similarity search - Function
Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / Nicotinic acetylcholine receptor / CD59 / CD59 / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Snake toxin-like superfamily ...Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxins signature. / Snake toxin, conserved site / 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, 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha / Alpha-bungarotoxin isoform V31
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bungarus multicinctus (many-banded krait)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsDellisanti, C.D. / Yao, Y. / Stroud, J.C. / Wang, Z. / Chen, L.
CitationJournal: Nat.Neurosci. / Year: 2007
Title: Crystal structure of the extracellular domain of nAChR alpha1 bound to alpha-bungarotoxin at 1.94 A resolution.
Authors: Dellisanti, C.D. / Yao, Y. / Stroud, J.C. / Wang, Z.Z. / Chen, L.
History
DepositionJun 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-bungarotoxin
B: Acetylcholine receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4843
Polymers32,7622
Non-polymers1,7221
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.498, 85.680, 95.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-bungarotoxin / Alpha-BTX V31 / BGTX V31 / Alpha-BgtV31 / Long neurotoxin 1


Mass: 8033.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bungarus multicinctus (many-banded krait) / References: UniProt: P60616
#2: Protein Acetylcholine receptor subunit alpha /


Mass: 24729.012 Da / Num. of mol.: 1 / Mutation: V8E, W149R, V155A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Chrna1, Acra / Production host: Escherichia coli (E. coli) / References: UniProt: P04756
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Na citrate, 18% 2-propanol, 8% PEG 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 26445 / Num. obs: 23030 / % possible obs: 87.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16 % / Biso Wilson estimate: 7.3 Å2 / Rsym value: 0.09 / Net I/σ(I): 20
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4 / Num. unique all: 2601 / Rsym value: 41 / % possible all: 67.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2BYP

2byp


Resolution: 1.94→41.59 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2255 -random
Rwork0.214 ---
all-26445 --
obs-23030 9.8 %-
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.424 Å20 Å20 Å2
2--4.576 Å20 Å2
3----4.152 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.94→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 116 187 2601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.614
X-RAY DIFFRACTIONc_dihedral_angle_d26.43
X-RAY DIFFRACTIONc_improper_angle_d0.9618
LS refinement shellResolution: 1.94→2.06 Å
RfactorNum. reflection% reflection
Rfree0.244 283 -
Rwork0.221 --
obs-2601 67.4 %

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