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- PDB-2wn9: Crystal structure of Aplysia ACHBP in complex with 4-0H-DMXBA -

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Basic information

Entry
Database: PDB / ID: 2wn9
TitleCrystal structure of Aplysia ACHBP in complex with 4-0H-DMXBA
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / 4-0H-DMXBA / ACETYLCHOLINE BINDING PROTEIN
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
Chem-ZY5 / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _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 23, 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)132,44312
Polymers129,8395
Non-polymers2,6047
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16900 Å2
ΔGint-64.13 kcal/mol
Surface area45230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.909, 115.394, 130.607
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)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ZY5 / 4-[(E)-5,6-DIHYDRO-2,3'-BIPYRIDIN-3(4H)-YLIDENEMETHYL]-3-METHOXYPHENOL


Mass: 294.348 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H18N2O2
#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.: 780 / 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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 26% PEG400, 0.1 M HEPES, PH 7.5, 0.2 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→56.8 Å / Num. obs: 132537 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BYN

2byn


Resolution: 1.75→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.847 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.1 / 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
Rfree0.20308 6584 5 %RANDOM
Rwork0.16965 ---
obs0.17131 125779 99.91 %-
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: 32.431 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2---0.73 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8406 0 185 780 9371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229064
X-RAY DIFFRACTIONr_bond_other_d0.0030.027902
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.97512403
X-RAY DIFFRACTIONr_angle_other_deg0.808318487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1151116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1424.345435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.029151483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5811558
X-RAY DIFFRACTIONr_chiral_restr0.090.21381
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021846
X-RAY DIFFRACTIONr_nbd_refined0.1930.21511
X-RAY DIFFRACTIONr_nbd_other0.1950.27815
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24443
X-RAY DIFFRACTIONr_nbtor_other0.0860.25435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2655
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0910.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.03635520
X-RAY DIFFRACTIONr_mcbond_other0.61932134
X-RAY DIFFRACTIONr_mcangle_it2.82848833
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.09144070
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.54863534
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 488 -
Rwork0.19 9127 -
obs--99.93 %
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)
10.6051-0.188-0.07410.647-0.34211.59560.04230.07880.0525-0.0594-0.0559-0.16680.08410.16630.0136-0.1155-0.01150.0253-0.04910.0113-0.04924.680111.618759.3299
21.33230.29960.35971.0862-0.16841.071-0.04720.10890.1367-0.11090.0080.1706-0.11330.02750.0392-0.08280.0142-0.0169-0.1165-0.0212-0.02960.196722.948160.3774
30.74320.09570.03371.5185-0.0520.49460.0173-0.0046-0.0303-0.10760.07680.20470.0497-0.1336-0.0941-0.1229-0.0179-0.0022-0.060.0102-0.0428-17.54993.350465.6533
41.20580.22020.28791.1690.32290.97890.02620.0631-0.1409-0.09350.05610.00740.1186-0.0223-0.0824-0.0348-0.0339-0.0188-0.11440.0033-0.0674-4.1257-19.689667.5374
50.77590.3086-0.37190.8026-0.38650.5312-0.05480.067-0.107-0.14160.0143-0.13710.1686-0.00750.0406-0.04640.05140.0154-0.0719-0.0159-0.060221.8722-13.941162.2797
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 208
2X-RAY DIFFRACTION2B-3 - 207
3X-RAY DIFFRACTION3C-5 - 208
4X-RAY DIFFRACTION4D-2 - 208
5X-RAY DIFFRACTION5E-8 - 207

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