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- PDB-2byn: Crystal structure of apo AChBP from Aplysia californica -

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Basic information

Entry
Database: PDB / ID: 2byn
TitleCrystal structure of apo AChBP from Aplysia californica
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / ACETYLCHOLINE BINDING PROTEIN / NICOTINIC ACETYLCHOLINE RECEPTOR / SOLUBLE ACETYLCHOLINE RECEPTOR / CONFORMATIONAL FLEXIBILITY
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / identical protein binding / membrane
Similarity search - Function
Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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
Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsHansen, S.B. / Sulzenbacher, G. / Huxford, T. / Marchot, P. / Taylor, P. / Bourne, Y.
CitationJournal: Embo J. / Year: 2005
Title: Structures of Aplysia Achbp Complexes with Nicotinic Agonists and Antagonists Reveal Distinctive Binding Interfaces and Conformations.
Authors: Hansen, S.B. / Sulzenbacher, G. / Huxford, T. / Marchot, P. / Taylor, P. / Bourne, Y.
History
DepositionAug 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 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 1.3Dec 13, 2023Group: 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,50011
Polymers129,2645
Non-polymers1,2366
Water15,889882
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)144.153, 146.768, 143.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-2154-

HOH

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE-BINDING PROTEIN


Mass: 25852.744 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) APLYSIA CALIFORNICA (California sea hare) / Cell: SENSORY CELL / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: 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.: 1
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.8 Å3/Da / Density % sol: 55.65 %
Crystal growpH: 5.6
Details: 12-14% PEG 4000, 0.1 M SODIUM CITRATE, PH 5.6, 20% ISOPROPANOL, 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 97846 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UX2

1ux2


Resolution: 2.02→40.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.514 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2980 3 %RANDOM
Rwork0.169 ---
obs0.17 94830 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2--2.49 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.02→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8512 0 82 882 9476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229037
X-RAY DIFFRACTIONr_bond_other_d0.0020.027892
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.95612319
X-RAY DIFFRACTIONr_angle_other_deg0.779318467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73651109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03324.286448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.505151496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.071562
X-RAY DIFFRACTIONr_chiral_restr0.0820.21358
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021834
X-RAY DIFFRACTIONr_nbd_refined0.1920.21603
X-RAY DIFFRACTIONr_nbd_other0.1970.27827
X-RAY DIFFRACTIONr_nbtor_refined0.1750.24303
X-RAY DIFFRACTIONr_nbtor_other0.0840.25245
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2845
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9051.55639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35728906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.88433980
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8364.53389
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.07 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.252 197
Rwork0.208 6255
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)
11.5360.179-0.27390.92390.27041.4643-0.01590.1425-0.0352-0.1435-0.03920.07340.0109-0.16880.0551-0.17340.0376-0.0169-0.12340.0142-0.220118.294634.7941-11.7967
21.18880.22520.06371.66820.00361.3676-0.015-0.0733-0.09260.0122-0.05780.14080.1162-0.19410.0728-0.250.02140.0268-0.0963-0.0724-0.17155.151929.140410.4635
31.79650.06360.29811.71870.02591.3439-0.0494-0.231-0.23760.1663-0.01280.0080.2049-0.07660.0622-0.13520.01420.0473-0.1143-0.0164-0.237822.855524.37129.9827
41.432-0.4475-0.13692.25430.02041.8462-0.0636-0.0328-0.15770.0620.092-0.21790.18920.2625-0.0283-0.20930.006-0.0399-0.1127-0.0506-0.160547.407626.729419.5267
51.32470.02870.09741.10290.29432.0938-0.02250.19-0.0887-0.03950.0647-0.08110.06410.0901-0.0422-0.2401-0.04940.0485-0.1033-0.0135-0.163844.65633.0657-6.2847
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 208
2X-RAY DIFFRACTION2B-5 - 207
3X-RAY DIFFRACTION3C-4 - 208
4X-RAY DIFFRACTION4D-5 - 208
5X-RAY DIFFRACTION5E-5 - 208

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