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- PDB-4ez1: Crystal structure of acetylcholine binding protein (AChBP) from A... -

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Basic information

Entry
Database: PDB / ID: 4ez1
TitleCrystal structure of acetylcholine binding protein (AChBP) from Aplysia Californica in complex with alpha-conotoxin BuIA
Components
  • Alpha-conotoxin BuIA
  • Soluble acetylcholine receptor
KeywordsCHOLINE BINDING PROTEIN/TOXIN / CHOLINE BINDING PROTEIN-TOXIN complex
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 / Alpha conotoxin precursor / 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 ...Conotoxin, alpha-type / Alpha conotoxin precursor / 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 BuIA / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Conus bullatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsTalley, T.T. / Reger, A.S. / Kim, C. / Sankaran, B. / Ho, K. / Taylor, P. / McIntosh, J.M.
CitationJournal: To be Published
Title: Pairwise interaction of alpha-conotoxin BuIA Pro6 with the beta subunit of nicotinic acetylcholine receptor
Authors: Filchakova, O.M. / Talley, T.T. / Reger, A.S. / Kim, C. / Ho, K. / Han, K. / Taylor, P. / McIntosh, J.M.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Structure summary

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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
K: Alpha-conotoxin BuIA
L: Alpha-conotoxin BuIA
M: Alpha-conotoxin BuIA
N: Alpha-conotoxin BuIA
O: Alpha-conotoxin BuIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,68811
Polymers137,63410
Non-polymers551
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21040 Å2
ΔGint-115 kcal/mol
Surface area40960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.437, 78.636, 117.636
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Soluble acetylcholine receptor / AChBP


Mass: 26212.105 Da / Num. of mol.: 5 / Fragment: UNP residues 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Plasmid: pFLAG-CMV-3 / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Protein/peptide
Alpha-conotoxin BuIA / Conotoxin Bu1.3


Mass: 1314.597 Da / Num. of mol.: 5 / Fragment: UNP residues 44-56 / Source method: obtained synthetically / Source: (synth.) Conus bullatus (invertebrata) / References: UniProt: P69657
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl, 0.25 M magnesium chloride, 20% w/v PEG4000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2002
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→45 Å / Num. all: 43898 / Num. obs: 41072 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.4
Reflection shellHighest resolution: 2.49 Å

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→45 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.529 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.516 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22713 2182 5 %RANDOM
Rwork0.17133 ---
obs0.17411 41072 98.52 %-
all-43351 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.905 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å2-1.26 Å2
2---0.93 Å2-0 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.49→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8512 0 1 201 8714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.028738
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.95311926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83451073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0224.59390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.721151355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9321540
X-RAY DIFFRACTIONr_chiral_restr0.0920.21349
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216653
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 149 -
Rwork0.22 2617 -
obs-3713 87.92 %

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