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- PDB-2wnj: CRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH DMXBA -

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Basic information

Entry
Database: PDB / ID: 2wnj
TitleCRYSTAL STRUCTURE OF APLYSIA ACHBP IN COMPLEX WITH DMXBA
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / ACETYLCHOLINE BINDING PROTEIN / DMXBA
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / identical protein binding / membrane / metal ion binding
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
Chem-ZY7 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSulzenbacher, G. / Hibbs, R. / Shi, J. / Talley, T. / Conrod, S. / Kem, W. / Taylor, P. / Marchot, P. / Bourne, Y.
CitationJournal: Embo J. / Year: 2009
Title: Structural Determinants for Interaction of Partial Agonists with Acetylcholine Binding Protein and Neuronal Alpha7 Nicotinic Acetylcholine Receptor.
Authors: Hibbs, R.E. / Sulzenbacher, G. / Shi, J. / Talley, T.T. / Conrod, S. / Kem, W.R. / Taylor, P. / Marchot, P. / Bourne, Y.
History
DepositionJul 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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_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.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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 9, 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
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)132,35112
Polymers129,8395
Non-polymers2,5127
Water17,871992
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15410 Å2
ΔGint-51.88 kcal/mol
Surface area44440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.222, 114.799, 131.284
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
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE BINDING PROTEIN


Mass: 25967.832 Da / Num. of mol.: 5 / Fragment: RESIDUES 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Cell: SENSORY CELL / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q8WSF8
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZY7 / (3E)-3-[(2,4-DIMETHOXYPHENYL)METHYLIDENE]-3,4,5,6-TETRAHYDRO-2,3'-BIPYRIDINE


Mass: 308.374 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H20N2O2 / Comment: agonist*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.: 992 / 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: 2.63 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 13% PEG4000, 0.1 M HEPES PH 7.5, 15% ISOPROPANOL, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.8→47 Å / Num. obs: 122269 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYN

2byn


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.749 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. GLOBAL B-FACTORS, CONTAINING RESIDUAL AND TLS COMPONENT HAVE BEEN DEPOSITED
RfactorNum. reflection% reflectionSelection details
Rfree0.20605 6066 5 %RANDOM
Rwork0.16855 ---
obs0.17042 116030 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.746 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---0.76 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8486 0 179 992 9657
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229336
X-RAY DIFFRACTIONr_bond_other_d0.0020.026274
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.98212788
X-RAY DIFFRACTIONr_angle_other_deg0.9033.00315297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32251154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77824.189444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.492151529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9981561
X-RAY DIFFRACTIONr_chiral_restr0.0940.21401
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210388
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021943
X-RAY DIFFRACTIONr_nbd_refined0.2010.21736
X-RAY DIFFRACTIONr_nbd_other0.220.26815
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24541
X-RAY DIFFRACTIONr_nbtor_other0.0990.25101
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2846
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0511.55628
X-RAY DIFFRACTIONr_mcbond_other0.2581.52157
X-RAY DIFFRACTIONr_mcangle_it1.59329019
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.29434285
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3664.53722
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: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 423 -
Rwork0.224 8436 -
obs--99.88 %
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)
11.0365-0.0955-0.05631.0994-0.21112.0370.01030.11110.1301-0.0954-0.0496-0.2307-0.01840.20320.0393-0.1749-0.02240.0229-0.167-0.0018-0.121824.902311.169759.4215
21.53870.16310.37951.2851-0.14021.64060.01160.12210.2039-0.099-0.02950.2281-0.1618-0.02970.0178-0.12930.02230.0067-0.2048-0.0309-0.06260.655922.85560.4957
30.8891-0.00830.05241.6520.04520.9857-0.01630.0338-0.0011-0.1530.00820.31420.0126-0.19330.008-0.1859-0.00590.0266-0.1347-0.0271-0.0761-17.26883.539865.5964
41.45820.27130.38881.37320.29981.53490.02870.1249-0.123-0.11820.02060.04830.1806-0.0301-0.0493-0.1366-0.01570.0024-0.1899-0.0154-0.1913-4.4243-19.322267.7741
51.14210.1419-0.44081.1691-0.37631.4435-0.06890.0986-0.0517-0.1331-0.0079-0.11690.12490.00840.0768-0.16180.02720.0082-0.1709-0.018-0.171221.9007-14.18162.3281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 208
2X-RAY DIFFRACTION2B-3 - 207
3X-RAY DIFFRACTION3C-5 - 207
4X-RAY DIFFRACTION4D-2 - 208
5X-RAY DIFFRACTION5E-8 - 207

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