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- PDB-1ux2: X-ray structure of acetylcholine binding protein (AChBP) -

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Basic information

Entry
Database: PDB / ID: 1ux2
TitleX-ray structure of acetylcholine binding protein (AChBP)
ComponentsACETYLCHOLINE BINDING PROTEIN
KeywordsGLYCOPROTEIN / PENTAMER / IGG FOLD / ACETYLCHOLINE / NICOTINE
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / 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
AMMONIUM ION / 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
DepositionFeb 18, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,63134
Polymers241,24810
Non-polymers4,38324
Water25,3111405
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)122,81517
Polymers120,6245
Non-polymers2,19112
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)122,81517
Polymers120,6245
Non-polymers2,19112
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)140.639, 140.639, 238.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.30253, -0.95314, -0.00073), (0.95289, 0.30247, -0.02251), (0.02168, 0.00611, 0.99975)73.12951, -9.99818, -1.23939
2given(-0.80879, -0.58776, 0.01978), (0.58728, -0.80898, -0.02552), (0.031, -0.00902, 0.99948)105.0232, 55.27438, -1.14149
3given(-0.804, 0.5939, 0.02955), (-0.5944, -0.80409, -0.01157), (0.01689, -0.02686, 0.9995)51.89292, 106.27448, 0.21597
4given(0.29742, 0.95454, 0.01998), (-0.95473, 0.29723, 0.0119), (0.00542, -0.02262, 0.99973)-12.5041, 72.48873, 0.81411
5given(0.00246, 0.99986, -0.0163), (0.99997, -0.00235, 0.0068), (0.00676, -0.01631, -0.99984)1.46616, -0.39631, 121.06586
6given(0.94793, 0.31525, -0.04525), (0.31571, -0.94885, 0.00327), (-0.0419, -0.01739, -0.99897)-8.77702, 71.96313, 123.07487
7given(0.59264, -0.80425, -0.04412), (-0.80409, -0.59394, 0.02591), (-0.04704, 0.02012, -0.99869)56.37846, 104.54358, 121.70767
8given(-0.58886, -0.80773, -0.02859), (-0.80819, 0.58809, 0.03121), (-0.00839, 0.04148, -0.9991)107.6067, 51.93881, 119.2374
9given(-0.95509, 0.29629, -0.00356), (0.29614, 0.95488, 0.0226), (0.0101, 0.02053, -0.99974)73.8439, -12.796, 119.18816

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Components

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Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJ

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


Mass: 24124.783 Da / Num. of mol.: 10
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
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1419 molecules

#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1405 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 8 / Details: TRIS PH 8.0, AMMONIUM SULFATE
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.4 Mammonium sulfate1reservoir
21 %PEG2001reservoir
30.1 MHEPES1reservoirpH7.0
40.1 MTris1droppH8.0

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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: 2.1→50 Å / Num. obs: 236373 / % possible obs: 99 % / Observed criterion σ(I): 1.3 / Redundancy: 13.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 1.3 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 50 Å / % possible obs: 99 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 99 % / Mean I/σ(I) obs: 1.3

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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: 7.866 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.232
RfactorNum. reflection% reflectionSelection details
Rfree0.28381 10023 7.3 %RANDOM
Rwork0.23583 ---
obs0.23948 184182 84.15 %-
Displacement parametersBiso mean: 23.461 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16515 0 274 1405 18194
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 12 Å / Num. reflection obs: 127031 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.012
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.32

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