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- PDB-5co5: Crystal structure of Ac-AChBP in complex with conotoxin GIC -

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Basic information

Entry
Database: PDB / ID: 5co5
TitleCrystal structure of Ac-AChBP in complex with conotoxin GIC
Components
  • Alpha-conotoxin GIC
  • Soluble acetylcholine receptor
KeywordsMETAL BINDING PROTEIN/TOXIN / AChBP / GIC / METAL 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 GIC / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
Conus geographus (geography cone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsWang, X.Q. / Xu, M.Y. / Luo, S.L. / Lin, B.
CitationJournal: To Be Published
Title: Crystal structure of Ac-AChBP in complex with conotoxin GIC
Authors: Wang, X.Q. / Xu, M.Y. / Luo, S.L. / Lin, B.
History
DepositionJul 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble acetylcholine receptor
F: Alpha-conotoxin GIC
B: Soluble acetylcholine receptor
C: Alpha-conotoxin GIC
D: Soluble acetylcholine receptor
E: Alpha-conotoxin GIC
G: Soluble acetylcholine receptor
H: Alpha-conotoxin GIC
I: Soluble acetylcholine receptor
J: Alpha-conotoxin GIC


Theoretical massNumber of molelcules
Total (without water)141,30410
Polymers141,30410
Non-polymers00
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20260 Å2
ΔGint-106 kcal/mol
Surface area43610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.585, 84.941, 208.601
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


Mass: 26645.967 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q8WSF8
#2: Protein/peptide
Alpha-conotoxin GIC


Mass: 1614.832 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Conus geographus (geography cone) / References: UniProt: Q86RB2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.5M lithium sulfate monohydrate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: BRUKER SMART 6500 / Detector: CCD / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 85409 / % possible obs: 96.9 % / Redundancy: 6.7 % / Net I/σ(I): 18.7

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementResolution: 2.1→43.453 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 4283 5.01 %
Rwork0.1784 --
obs0.1806 85409 96.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8810 0 0 648 9458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089040
X-RAY DIFFRACTIONf_angle_d1.15312295
X-RAY DIFFRACTIONf_dihedral_angle_d13.243275
X-RAY DIFFRACTIONf_chiral_restr0.051370
X-RAY DIFFRACTIONf_plane_restr0.0061600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0515-2.07480.30031250.23122522X-RAY DIFFRACTION90
2.0748-2.09920.27751390.22312557X-RAY DIFFRACTION94
2.0992-2.12480.29061390.22742585X-RAY DIFFRACTION93
2.1248-2.15170.2621070.21672590X-RAY DIFFRACTION94
2.1517-2.180.26231340.21832615X-RAY DIFFRACTION93
2.18-2.20990.26051310.22182583X-RAY DIFFRACTION94
2.2099-2.24140.3081410.22112563X-RAY DIFFRACTION93
2.2414-2.27490.26271480.21582612X-RAY DIFFRACTION95
2.2749-2.31040.2941450.21722613X-RAY DIFFRACTION94
2.3104-2.34830.24321370.20522621X-RAY DIFFRACTION96
2.3483-2.38880.27291400.20242602X-RAY DIFFRACTION95
2.3888-2.43220.2611130.20662719X-RAY DIFFRACTION96
2.4322-2.4790.27471500.20842636X-RAY DIFFRACTION96
2.479-2.52960.27521630.20322658X-RAY DIFFRACTION96
2.5296-2.58460.24321530.19862678X-RAY DIFFRACTION97
2.5846-2.64470.23551580.19422714X-RAY DIFFRACTION98
2.6447-2.71090.23441540.19532709X-RAY DIFFRACTION98
2.7109-2.78410.26511440.19542726X-RAY DIFFRACTION99
2.7841-2.8660.22891290.19632762X-RAY DIFFRACTION99
2.866-2.95850.28011420.19922771X-RAY DIFFRACTION99
2.9585-3.06430.2471440.20192769X-RAY DIFFRACTION99
3.0643-3.18690.23221380.19562779X-RAY DIFFRACTION99
3.1869-3.33190.25461430.18482796X-RAY DIFFRACTION100
3.3319-3.50750.21021360.17962829X-RAY DIFFRACTION100
3.5075-3.72710.20951440.16792806X-RAY DIFFRACTION100
3.7271-4.01470.20611460.15862798X-RAY DIFFRACTION100
4.0147-4.41840.14971620.13222826X-RAY DIFFRACTION100
4.4184-5.05690.14321470.12552844X-RAY DIFFRACTION100
5.0569-6.3680.1891560.15972888X-RAY DIFFRACTION100
6.368-43.46240.23251750.18172955X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 5.0676 Å / Origin y: -35.3219 Å / Origin z: 27.5531 Å
111213212223313233
T0.1935 Å20.0058 Å2-0.0017 Å2-0.1381 Å2-0.0346 Å2--0.181 Å2
L0.5364 °20.0261 °20.0034 °2-0.2737 °2-0.2987 °2--0.5925 °2
S0.0168 Å °0.0008 Å °-0.0502 Å °0.0069 Å °0.0108 Å °0.016 Å °0.022 Å °-0.0165 Å °0 Å °
Refinement TLS groupSelection details: all

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