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- PDB-1uw6: X-ray structure of acetylcholine binding protein (AChBP) in compl... -

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Basic information

Entry
Database: PDB / ID: 1uw6
TitleX-ray structure of acetylcholine binding protein (AChBP) in complex with nicotine
ComponentsACETYLCHOLINE-BINDING PROTEIN
KeywordsGLYCOPROTEIN / PENTAMER / IGG FOLD / ACETYLCHOLINE / NICOTINE
Function / homology
Function and homology information


synaptic cleft / extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / synapse / membrane
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 / Ig-like domain profile. / Immunoglobulin-like domain / Mainly Beta
Similarity search - Domain/homology
(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLYMNAEA STAGNALIS (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCelie, P.H.N. / Van Rossum-fikkert, S.E. / Van Dijk, W.J. / Brejc, K. / Smit, A.B. / Sixma, T.K.
Citation
Journal: Neuron / Year: 2004
Title: Nicotine and Carbamylcholine Binding to Nicotinic Acetylcholine Receptors as Studied in Achbp Crystal Structures
Authors: Celie, P.H.N. / Van Rossum-Fikkert, S.E. / Van Dijk, W.J. / Brejc, K. / Smit, A.B. / Sixma, T.K.
#1: Journal: Nature / Year: 2001
Title: Crystal Structure of an Ach-Binding Protein Reveals the Ligand-Binding Domain of Nicotinic Receptors
Authors: Brejc, K. / Van Dijk, W.J. / Klaassen, R. / Schuurmans, M. / Van Der Oost, J. / Smit, A.B. / Sixma, T.K.
#2: Journal: Nature / Year: 2001
Title: A Glia-Derived Acetylcholine-Binding Protein that Modulates Synaptic Transmission
Authors: Smit, A.B. / Syed, N.I. / Schaap, D. / Van Minnen, J. / Klumperman, J. / Kits, K.S. / Lodder, H. / Van Der Schors, R.C. / Van Elk, R. / Sorgedrager, B. / Brejc, K. / Sixma, T.K. / Geraerts, W.P.M.
History
DepositionJan 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLCHOLINE-BINDING PROTEIN
B: ACETYLCHOLINE-BINDING PROTEIN
C: ACETYLCHOLINE-BINDING PROTEIN
D: ACETYLCHOLINE-BINDING PROTEIN
E: ACETYLCHOLINE-BINDING PROTEIN
F: ACETYLCHOLINE-BINDING PROTEIN
G: ACETYLCHOLINE-BINDING PROTEIN
H: ACETYLCHOLINE-BINDING PROTEIN
I: ACETYLCHOLINE-BINDING PROTEIN
J: ACETYLCHOLINE-BINDING PROTEIN
K: ACETYLCHOLINE-BINDING PROTEIN
L: ACETYLCHOLINE-BINDING PROTEIN
M: ACETYLCHOLINE-BINDING PROTEIN
N: ACETYLCHOLINE-BINDING PROTEIN
O: ACETYLCHOLINE-BINDING PROTEIN
P: ACETYLCHOLINE-BINDING PROTEIN
Q: ACETYLCHOLINE-BINDING PROTEIN
R: ACETYLCHOLINE-BINDING PROTEIN
S: ACETYLCHOLINE-BINDING PROTEIN
T: ACETYLCHOLINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)483,75840
Polymers480,51320
Non-polymers3,24520
Water26,4641469
1
A: ACETYLCHOLINE-BINDING PROTEIN
B: ACETYLCHOLINE-BINDING PROTEIN
C: ACETYLCHOLINE-BINDING PROTEIN
D: ACETYLCHOLINE-BINDING PROTEIN
E: ACETYLCHOLINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,93910
Polymers120,1285
Non-polymers8115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
F: ACETYLCHOLINE-BINDING PROTEIN
G: ACETYLCHOLINE-BINDING PROTEIN
H: ACETYLCHOLINE-BINDING PROTEIN
I: ACETYLCHOLINE-BINDING PROTEIN
J: ACETYLCHOLINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,93910
Polymers120,1285
Non-polymers8115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
K: ACETYLCHOLINE-BINDING PROTEIN
L: ACETYLCHOLINE-BINDING PROTEIN
M: ACETYLCHOLINE-BINDING PROTEIN
N: ACETYLCHOLINE-BINDING PROTEIN
O: ACETYLCHOLINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,93910
Polymers120,1285
Non-polymers8115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
P: ACETYLCHOLINE-BINDING PROTEIN
Q: ACETYLCHOLINE-BINDING PROTEIN
R: ACETYLCHOLINE-BINDING PROTEIN
S: ACETYLCHOLINE-BINDING PROTEIN
T: ACETYLCHOLINE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,93910
Polymers120,1285
Non-polymers8115
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)233.000, 267.422, 73.139
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11O-2043-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999, 0.036, -0.017), (0.006, 0.3, 0.954), (0.039, -0.953, 0.3)-3.38885, 55.19213, 85.36037
2given(0.998, 0.048, 0.031), (0.021, -0.807, 0.59), (0.054, -0.588, -0.807)-4.46955, 154.03006, 59.52009
3given(0.998, 0.008, 0.055), (0.039, -0.806, -0.591), (0.039, 0.592, -0.805)-0.98504, 160.04492, -43.40739
4given(1, -0.017, 0.017), (0.021, 0.315, -0.949), (0.011, 0.949, 0.315)1.15079, 64.88787, -79.85012
5given(1, -0.002, 0.007), (0.007, 0.615, -0.789), (-0.003, 0.789, 0.615)0.3816, 103.29865, -29.39178
6given(1, 0.022, -0.001), (-0.021, 0.941, 0.339), (0.009, -0.339, 0.941)-1.64371, 69.33533, 67.11072
7given(0.999, 0.036, 0.022), (-0.02, -0.037, 0.999), (0.037, -0.999, -0.036)-2.97321, 151.13936, 129.27414
8given(0.999, 0.018, 0.044), (0.006, -0.965, 0.261), (0.047, -0.26, -0.964)-1.54382, 235.29132, 69.18992
9given(1, -0.003, 0.028), (0.022, -0.566, -0.824), (0.019, 0.825, -0.565)0.25321, 206.24313, -26.93529
10given(0.999, 0.043, 0.019), (-0.01, -0.217, 0.976), (0.046, -0.975, -0.216)-4.09576, 32.3143, 113.92276
11given(0.999, 0.015, 0.042), (0.01, -0.995, 0.1), (0.044, -0.099, -0.994)-1.74565, 105.29977, 41.98955
12given(0.999, -0.013, 0.032), (0.024, -0.381, -0.924), (0.024, 0.924, -0.381)0.72234, 56.71478, -50.2866
13given(1, 0.004), (0.002, 0.757, -0.653), (-0.003, 0.653, 0.757)-0.23727, -43.69649, -31.87772
14given(1, 0.023, -0.007), (-0.016, 0.865, 0.502), (0.018, -0.502, 0.865)-2.25292, -59.50208, 67.60023
15given(0.999, 0.004, 0.044), (0.016, -0.964, -0.265), (0.041, 0.266, -0.963)-0.52434, 306.81171, 47.70136
16given(1, -0.016, 0.01), (0.009, -0.058, -0.998), (0.017, 0.998, -0.057)1.33447, 232.44279, -21.13311
17given(1, 0.009, -0.009), (-0.011, 0.934, -0.356), (0.005, 0.357, 0.934)-0.60248, 142.60065, 29.89751
18given(0.999, 0.044, -0.006), (-0.023, 0.623, 0.782), (0.038, -0.781, 0.623)-3.88376, 163.75378, 129.5831
19given(0.999, 0.04, 0.036), (-0.01, -0.523, 0.852), (0.052, -0.851, -0.522)-3.71114, 263.30035, 142.72557

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Components

#1: Protein
ACETYLCHOLINE-BINDING PROTEIN / ACH-BINDING PROTEIN / ACHBP


Mass: 24025.652 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LYMNAEA STAGNALIS (great pond snail) / Plasmid: PPIC9 / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): GS 115 / References: UniProt: P58154
#2: Chemical
ChemComp-NCT / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / (S)-(-)-NICOTINE / 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE


Mass: 162.232 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C10H14N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1469 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 8 / Details: TRIS PH 8.0, AMMONIUM SULFATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MTris1droppH8.0
20.8 mMNicotine1drop
310 mg/mlAChBP1drop
42.1 Mammonium sulfate1reservoir
51 %PEG2001reservoir
60.1 MTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 236373 / % possible obs: 86 % / Observed criterion σ(I): 1.7 / Redundancy: 2.9 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.89 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 1.7 / % possible all: 38
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / % possible obs: 86 % / Redundancy: 8 % / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
% possible obs: 38 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I9B

1i9b


Resolution: 2.2→12 Å / SU B: 8.062 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.462 / ESU R Free: 0.273
RfactorNum. reflection% reflectionSelection details
Rfree0.26533 9739 5 %RANDOM
Rwork0.22164 ---
obs0.22386 184182 84.15 %-
Displacement parametersBiso mean: 21.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20 Å2
2--0.46 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33079 0 240 1469 34788
Refinement
*PLUS
Lowest resolution: 12 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.015
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.46

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