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- PDB-2byp: Crystal structure of Aplysia californica AChBP in complex with al... -

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Basic information

Entry
Database: PDB / ID: 2byp
TitleCrystal structure of Aplysia californica AChBP in complex with alpha- conotoxin ImI
Components
  • ALPHA-CONOTOXIN IMI
  • SOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / RECEPTOR COMPLEX / NICOTINIC ACETYLCHOLINE RECEPTOR COMPLEX / CONOTOXIN
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor activity / ion channel regulator activity / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / toxin activity / extracellular region / membrane / identical protein binding / metal ion binding
Similarity search - Function
Conotoxin, alpha-type, conserved site / Alpha-conotoxin family signature. / 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
Alpha-conotoxin ImI / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
CONUS IMPERIALIS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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: Refinement description / 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 1.3Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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
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
F: ALPHA-CONOTOXIN IMI
G: ALPHA-CONOTOXIN IMI
H: ALPHA-CONOTOXIN IMI
I: ALPHA-CONOTOXIN IMI
J: ALPHA-CONOTOXIN IMI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,60911
Polymers128,38810
Non-polymers2211
Water18,7721042
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21320 Å2
ΔGint-109.4 kcal/mol
Surface area45330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.284, 140.036, 153.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11E-2004-

HOH

21E-2043-

HOH

31E-2044-

HOH

41E-2062-

HOH

51E-2120-

HOH

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Components

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


Mass: 24320.039 Da / Num. of mol.: 5
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) / Tissue (production host): KIDNEY / References: UniProt: Q8WSF8
#2: Protein/peptide
ALPHA-CONOTOXIN IMI


Mass: 1357.609 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) CONUS IMPERIALIS (invertebrata) / References: UniProt: P50983
#3: 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 / N-Acetylglucosamine


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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 2.44 Å3/Da / Density % sol: 49.25 %
Crystal growpH: 7.5 / Details: 11-14% PEG-4000, 0.1 M TRIS, PH 7.5, 0.4 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.976
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 86601 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 29.5

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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 2BYN

2byn


Resolution: 2.07→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.782 / SU ML: 0.122 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1700 2 %RANDOM
Rwork0.173 ---
obs0.174 83709 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2---0.84 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.07→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8865 0 14 1042 9921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229428
X-RAY DIFFRACTIONr_bond_other_d0.0020.028235
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9512844
X-RAY DIFFRACTIONr_angle_other_deg0.837319238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23851103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.124.03469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.305151579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6951570
X-RAY DIFFRACTIONr_chiral_restr0.0850.21440
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021936
X-RAY DIFFRACTIONr_nbd_refined0.1850.21438
X-RAY DIFFRACTIONr_nbd_other0.1930.27916
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24302
X-RAY DIFFRACTIONr_nbtor_other0.0830.25258
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2839
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0081.57321
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19429301
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.80234491
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5884.53543
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: 2.07→2.12 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 121
Rwork0.231 5925
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)
11.04920.2472-0.25622.27710.40461.9019-0.02190.0138-0.00790.3415-0.01830.21140.1032-0.23440.0402-0.1962-0.00710.0064-0.18390.0245-0.253831.925728.695973.0441
20.95180.14520.37891.72390.24331.90970.0217-0.0646-0.0171-0.0618-0.04180.16250.2447-0.18370.0201-0.2325-0.0051-0.0059-0.2523-0.0209-0.2133.998918.150948.1371
30.9377-0.3460.23671.7509-0.11061.11110.06380.0906-0.0141-0.2627-0.04010.12430.0385-0.0261-0.0237-0.21960.00360.0016-0.220.0013-0.259434.090338.23730.0962
41.4195-0.0350.08312.3659-0.03241.94640.03080.05880.1223-0.004-0.05020.2281-0.3241-0.19970.0194-0.1820.00450.0181-0.28210.0173-0.205131.857861.594743.4093
50.7848-0.14450.29581.8369-0.68731.9583-0.0571-0.0656-0.01510.60760.13820.218-0.5881-0.1972-0.0810.04090.05270.086-0.2037-0.0042-0.215630.03755.690670.4029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 208
2X-RAY DIFFRACTION2B-4 - 208
3X-RAY DIFFRACTION3C-2 - 208
4X-RAY DIFFRACTION4D0 - 208
5X-RAY DIFFRACTION5E-5 - 208

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