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- PDB-2xyt: Crystal structure of Aplysia californica AChBP in complex with d-... -

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Basic information

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


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / 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
D-TUBOCURARINE / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,93915
Polymers246,88610
Non-polymers3,0545
Water27,2031510
1
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)124,6647
Polymers123,4435
Non-polymers1,2212
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint-74 kcal/mol
Surface area42240 Å2
MethodPISA
2
F: SOLUBLE ACETYLCHOLINE RECEPTOR
G: SOLUBLE ACETYLCHOLINE RECEPTOR
H: SOLUBLE ACETYLCHOLINE RECEPTOR
I: SOLUBLE ACETYLCHOLINE RECEPTOR
J: SOLUBLE ACETYLCHOLINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,2758
Polymers123,4435
Non-polymers1,8323
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14010 Å2
ΔGint-74.3 kcal/mol
Surface area42340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.423, 137.595, 236.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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


Mass: 24688.578 Da / Num. of mol.: 10 / 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-TC9 / D-TUBOCURARINE / Tubocurarine chloride


Mass: 610.739 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C37H42N2O6 / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1510 / 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: 2.72 Å3/Da / Density % sol: 54.75 % / Description: NONE
Crystal growDetails: 200 MM NA2 SO4, 100 MM BISTRISPROPANE PH 8.5, 15% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.05→48.43 Å / Num. obs: 170800 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 29.683 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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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: 2.05→45.539 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 20.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 8277 5 %
Rwork0.1759 --
obs0.1782 165705 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.963 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 35.12 Å2
Baniso -1Baniso -2Baniso -3
1-3.9359 Å20 Å20 Å2
2---1.2358 Å20 Å2
3----2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16358 0 225 1510 18093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718122
X-RAY DIFFRACTIONf_angle_d1.09224904
X-RAY DIFFRACTIONf_dihedral_angle_d20.8046793
X-RAY DIFFRACTIONf_chiral_restr0.0742710
X-RAY DIFFRACTIONf_plane_restr0.0053214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12330.26347430.204914554X-RAY DIFFRACTION90
2.1233-2.20830.25798290.186715056X-RAY DIFFRACTION94
2.2083-2.30880.2577710.188715176X-RAY DIFFRACTION94
2.3088-2.43050.23378000.173115590X-RAY DIFFRACTION97
2.4305-2.58280.23448040.182615860X-RAY DIFFRACTION98
2.5828-2.78210.2548640.188815896X-RAY DIFFRACTION98
2.7821-3.06210.22968450.177316087X-RAY DIFFRACTION99
3.0621-3.5050.21678680.173916211X-RAY DIFFRACTION100
3.505-4.41540.18498610.148516335X-RAY DIFFRACTION100
4.4154-45.55070.1828920.154716663X-RAY DIFFRACTION99
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)
10.81690.05090.12020.4698-0.22911.1828-0.0570.0133-0.067-0.12680.06810.15180.0814-0.1261-0.01520.1353-0.0663-0.04130.17020.0120.18760.6019116.587535.0357
20.9999-0.13870.27830.6562-0.24140.81080.0014-0.0312-0.0522-0.00370.0401-0.00250.05850.0266-0.04010.0781-0.00510.00730.12820.01610.140821.2039117.499852.1716
30.97370.14050.19550.5960.20231.2586-0.03840.0298-0.1012-0.14520.0406-0.22910.1540.14770.02380.08340.04230.06480.08470.00050.122144.1002119.200437.9498
40.8187-0.0581-0.17541.1169-0.22111.0651-0.09770.1448-0.047-0.47350.0994-0.07390.09220.04060.0120.2983-0.01230.10160.13-0.05290.108337.263118.730411.9188
50.896-0.074-0.00450.392-0.13050.8768-0.09150.1172-0.0697-0.41670.13140.12440.196-0.1154-0.04550.3975-0.1026-0.06670.1757-0.02910.123410.5437116.838910.0831
60.9719-0.2208-0.08960.94860.04791.1366-0.0682-0.09690.0040.3060.1127-0.0309-0.1266-0.0332-0.03220.30330.0288-0.01010.1413-0.01920.029154.6069110.3617108.4488
70.5464-0.1275-0.15010.7388-0.26811.1107-0.025-0.020.01870.11370.03440.1399-0.1137-0.1089-0.02260.13880.0330.02470.16120.02590.136341.7141110.682585.1353
80.61890.2786-0.09071.0729-0.06620.6263-0.02340.0589-0.01640.01410.0277-0.109-0.0360.01220.00790.0738-0.0124-0.01330.12910.03550.119860.1635109.387665.4736
90.51850.04320.03980.61950.02510.8723-0.047-0.0176-0.01510.1780.0254-0.2635-0.04860.17540.01730.0554-0.0489-0.05570.13930.01390.169184.5028108.420177.1512
100.9195-0.11020.06640.7899-0.25071.1533-0.0225-0.14380.01880.3524-0.0381-0.1566-0.13390.09060.06160.2359-0.0619-0.13520.19660.00930.144281.0728108.7582103.6387
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
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J

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