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- PDB-5jme: Crystal structure of acetylcholine binding protein (AChBP) from A... -

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Basic information

Entry
Database: PDB / ID: 5jme
TitleCrystal structure of acetylcholine binding protein (AChBP) from Aplysia Californica in complex with alpha-conotoxin PeIA
Components
  • Soluble acetylcholine receptor
  • alpha-conotoxin PeIA from Conus pergrandis
KeywordsACETYLCHOLINE BINDING PROTEIN / AChBP / Conotoxin / Nicotinic
Function / homology
Function and homology information


host cell postsynaptic membrane / acetylcholine receptor inhibitor 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 / 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 PeIA / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Conus pergrandis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.336 Å
AuthorsBobango, J. / Sankaran, B. / McIntosh, J.M. / Talley, T.T.
CitationJournal: To Be Published
Title: Crystal structure of acetylcholine binding protein (AChBP) from Aplysia Californica in complex with alpha-conotoxin PeIA
Authors: Bobango, J. / McIntosh, J.M. / Sankaran, B. / Talley, T.T.
History
DepositionApr 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 PeIA from Conus pergrandis
G: alpha-conotoxin PeIA from Conus pergrandis
H: alpha-conotoxin PeIA from Conus pergrandis
I: alpha-conotoxin PeIA from Conus pergrandis


Theoretical massNumber of molelcules
Total (without water)137,6889
Polymers137,6889
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18470 Å2
ΔGint-95 kcal/mol
Surface area42220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.115, 147.890, 146.309
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Soluble acetylcholine receptor


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)
Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Protein/peptide
alpha-conotoxin PeIA from Conus pergrandis


Mass: 1656.908 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: C-terminal is aminated / Source: (synth.) Conus pergrandis (invertebrata) / References: UniProt: Q1L777*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.85 Å3/Da / Density % sol: 61.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl, 0.25 M magnesium chloride, 20% w/v PEG4000

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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: Oct 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.336→48.821 Å / Num. obs: 66090 / % possible obs: 92.6 % / Redundancy: 14.75 % / Biso Wilson estimate: 36.0398620104 Å2 / Net I/σ(I): 3.51

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EZ1

4ez1


Resolution: 2.336→48.821 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 2000 3.03 %
Rwork0.1959 64051 -
obs0.1969 66051 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.75 Å2 / Biso mean: 39.913 Å2 / Biso min: 18.69 Å2
Refinement stepCycle: final / Resolution: 2.336→48.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8396 0 0 332 8728
Biso mean---38.66 -
Num. residues----1100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088653
X-RAY DIFFRACTIONf_angle_d0.9911862
X-RAY DIFFRACTIONf_chiral_restr0.0581353
X-RAY DIFFRACTIONf_plane_restr0.0071536
X-RAY DIFFRACTIONf_dihedral_angle_d12.7765185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3363-2.39470.27821250.22964042416788
2.3947-2.45950.3031430.22734540468399
2.4595-2.53180.26921430.229445424685100
2.5318-2.61360.2771340.232545594693100
2.6136-2.7070.28071470.236545904737100
2.707-2.81530.29781430.221646044747100
2.8153-2.94350.28711430.219845764719100
2.9435-3.09860.22361420.209545984740100
3.0986-3.29270.21181450.196945984743100
3.2927-3.54690.21891460.191646164762100
3.5469-3.90370.2211450.182146254770100
3.9037-4.46820.18781460.162246474793100
4.4682-5.62820.18671430.166146994842100
5.6282-48.83180.23061550.207848154970100

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