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- PDB-2xys: Crystal structure of Aplysia californica AChBP in complex with st... -

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Basic information

Entry
Database: PDB / ID: 2xys
TitleCrystal structure of Aplysia californica AChBP in complex with strychnine
ComponentsSOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR / AMIDATION / CONFORMATIONAL FLEXIBILITY / CONOTOXIN / NEUROTOXIN / NICOTINIC / POSTSYNAPTIC NEUROTOXIN / RECEPTOR-TOXIN COMPLEX
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / neuron projection / synapse / identical protein binding / membrane / metal ion binding
Similarity search - Function
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
STRYCHNINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.909 Å
AuthorsBrams, M. / Pandya, A. / Kuzmin, D. / van Elk, R. / Krijnen, L. / Yakel, J.L. / Tsetlin, V. / Smit, A.B. / Ulens, C.
CitationJournal: Plos Biol. / Year: 2011
Title: A Structural and Mutagenic Blueprint for Molecular Recognition of Strychnine and D-Tubocurarine by Different Cys-Loop Receptors.
Authors: Brams, M. / Pandya, A. / Kuzmin, D. / Van Elk, R. / Krijnen, L. / Yakel, J.L. / Tsetlin, V. / Smit, A.B. / Ulens, C.
History
DepositionNov 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,44911
Polymers123,4435
Non-polymers2,0066
Water19,9071105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-72.6 kcal/mol
Surface area41740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.593, 100.593, 289.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-2018-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.029, -0.004), (-0.024, 0.725, 0.689), (-0.017, 0.689, -0.725)
Vector: 52.963, 0.539, 0.403)

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACHBP


Mass: 24688.578 Da / Num. of mol.: 5 / Fragment: RESIDUES 20-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-SY9 / STRYCHNINE


Mass: 334.412 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H22N2O2 / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1105 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 % / Description: NONE
Crystal growDetails: 200 MM SODIUM ACETATE, 100 MM BISTRISPROPANE AT PH 8.5, 15.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.91→49.56 Å / Num. obs: 113796 / % possible obs: 98.2 % / Observed criterion σ(I): 1.3 / Redundancy: 5.6 % / Biso Wilson estimate: 21.93 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.3 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UZ6

2uz6


Resolution: 1.909→44.608 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 19.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2097 5414 5 %
Rwork0.1718 --
obs0.1738 107844 92.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.347 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 26.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.6395 Å20 Å20 Å2
2---1.6395 Å20 Å2
3---3.2789 Å2
Refinement stepCycle: LAST / Resolution: 1.909→44.608 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8180 0 150 1105 9435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078806
X-RAY DIFFRACTIONf_angle_d1.19412102
X-RAY DIFFRACTIONf_dihedral_angle_d15.5583248
X-RAY DIFFRACTIONf_chiral_restr0.0791365
X-RAY DIFFRACTIONf_plane_restr0.0051554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.909-1.97720.28984370.2498002X-RAY DIFFRACTION74
1.9772-2.05640.25645020.20049539X-RAY DIFFRACTION88
2.0564-2.150.24655200.17659989X-RAY DIFFRACTION92
2.15-2.26330.20865200.170710233X-RAY DIFFRACTION94
2.2633-2.40510.22585090.171110484X-RAY DIFFRACTION96
2.4051-2.59080.21545510.170510583X-RAY DIFFRACTION96
2.5908-2.85150.23385700.174110657X-RAY DIFFRACTION97
2.8515-3.2640.20185940.17210824X-RAY DIFFRACTION98
3.264-4.11190.1815870.149510926X-RAY DIFFRACTION98
4.1119-44.61980.17856240.158311193X-RAY DIFFRACTION96
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)
10.67930.20760.07710.74890.15050.75520.02960.07520.007-0.1633-0.0195-0.11850.0490.0662-0.00480.0970.00320.04720.1037-0.00890.0995-31.857619.8121-11.5998
20.51310.2608-0.20270.55790.0870.6606-0.01930.0164-0.1171-0.04050.02470.05910.0441-0.03060.01620.125-0.00390.0170.0546-0.01920.0989-51.33512.0946-6.9384
30.59870.3034-0.04730.6120.17870.7451-0.0023-0.1371-0.0390.0649-0.02260.06030.0906-0.0696-0.00610.1274-0.01080.02750.10390.02310.0777-58.92354.296818.8068
40.60530.2335-0.06860.91270.00820.62380.0193-0.1860.09620.1145-0.02-0.0398-0.01510.00090.00350.08950.0032-0.00150.1468-0.00740.0538-44.162523.651729.8927
50.66520.2446-0.15920.41810.07670.8950.0261-0.02570.04070.0167-0.0186-0.0946-0.05840.0567-0.00360.0168-0.0140.00260.0699-0.00530.075-27.277433.27711.1605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

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