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- PDB-2c9t: Crystal Structure Of Acetylcholine Binding Protein (AChBP) From A... -

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Basic information

Entry
Database: PDB / ID: 2c9t
TitleCrystal Structure Of Acetylcholine Binding Protein (AChBP) From Aplysia Californica In Complex With alpha-Conotoxin ImI
Components
  • ALPHA-CONOTOXIN IMI
  • SOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR/TOXIN / RECEPTOR-TOXIN COMPLEX / ACETYLCHOLINE BINDING PROTEIN / NICOTINIC ACETYLCHOLINE RECEPTOR-TOXIN COMPLEX / CONFORMATIONAL FLEXIBILITY / CONOTOXIN / ACETYLCHOLINE RECEPTOR INHIBITOR / AMIDATION / NEUROTOXIN / POSTSYNAPTIC NEUROTOXIN / TOXIN
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 / metal ion binding / identical protein binding / membrane
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: 2.25 Å
AuthorsUlens, C. / Hogg, R.C. / Celie, P.H. / Bertrand, D. / Tsetlin, V. / Smit, A.B. / Sixma, T.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Structural Determinants of Selective {Alpha}-Conotoxin Binding to a Nicotinic Acetylcholine Receptor Homolog Achbp.
Authors: Ulens, C. / Hogg, R.C. / Celie, P.H. / Bertrand, D. / Tsetlin, V. / Smit, A.B. / Sixma, T.K.
History
DepositionDec 14, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
K: ALPHA-CONOTOXIN IMI
M: ALPHA-CONOTOXIN IMI
O: ALPHA-CONOTOXIN IMI
P: ALPHA-CONOTOXIN IMI
Q: ALPHA-CONOTOXIN IMI
R: ALPHA-CONOTOXIN IMI
S: ALPHA-CONOTOXIN IMI
T: ALPHA-CONOTOXIN IMI


Theoretical massNumber of molelcules
Total (without water)257,73918
Polymers257,73918
Non-polymers00
Water27,2751514
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.211, 123.131, 118.749
Angle α, β, γ (deg.)90.00, 117.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.723, 0.691, 0.008), (-0.33, 0.355, -0.875), (-0.607, 0.63, 0.484)
Vector: -2.77167, 34.79053, 16.77406)

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE BINDING PROTEIN


Mass: 24688.578 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Details: ALPHA-CONOTOXIN IMI BOUND IN RECEPTOR SITES / Source: (natural) APLYSIA CALIFORNICA (California sea hare) / References: UniProt: Q8WSF8
#2: Protein/peptide
ALPHA-CONOTOXIN IMI / ALPHA-CTX IMI


Mass: 1356.601 Da / Num. of mol.: 8 / Fragment: RESIDUES 5-16 / Source method: isolated from a natural source / Details: ALPHA-CONOTOXIN IMI BOUND IN RECEPTOR SITES / Source: (natural) CONUS IMPERIALIS (invertebrata) / References: UniProt: P50983
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1514 / Source method: isolated from a natural source / Formula: H2O
Compound detailsALPHA-CONOTOXINS INHIBIT THE NICOTINIC ACETYLCHOLINE RECEPTORS (NACHR) ON THE POSTSYNAPTIC MEMBRANES
Has protein modificationY
Sequence detailsSEQUENCE HAS BEEN DEPOSITED ALONG WITH THE CRYSTAL STRUCTURE IN THE PROTEIN DATA BANK.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.8 %
Description: ALPHA-CONOTOXINS WERE REMOVED FROM THE SEARCH MODEL TO REDUCE MODEL BIAS.
Crystal growDetails: 100 MM SODIUM ACETATE PH 5.5, 12.5% PEG5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.25→54.07 Å / Num. obs: 135691 / % possible obs: 99.2 % / Observed criterion σ(I): 1.4 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BR8

2br8


Resolution: 2.25→105.41 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.917 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ASYMMETRIC UNIT CONTAINS TWO PENTAMERS. ONE PENTAMER HAS 3 ALPHA-CONOTOXINS BOUND, THE OTHER PENTAMER HAS 5 ALPHA-CONTOXINS BOUND.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 6818 5 %RANDOM
Rwork0.168 ---
obs0.171 128836 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.05 Å2
2--0.55 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.25→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17088 0 0 1514 18602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02217543
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215244
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.9523947
X-RAY DIFFRACTIONr_angle_other_deg0.872335583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46952130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19724.282822
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.377152825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.92815106
X-RAY DIFFRACTIONr_chiral_restr0.0890.22660
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023545
X-RAY DIFFRACTIONr_nbd_refined0.1960.23108
X-RAY DIFFRACTIONr_nbd_other0.1980.215811
X-RAY DIFFRACTIONr_nbtor_refined0.1780.28262
X-RAY DIFFRACTIONr_nbtor_other0.0890.210269
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.21414
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3020.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.11.513704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.296217609
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.11138073
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0734.56337
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: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.3 464
Rwork0.22 9490

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