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- PDB-2br8: Crystal Structure of Acetylcholine-binding Protein (AChBP) from A... -

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Basic information

Entry
Database: PDB / ID: 2br8
TitleCrystal Structure of Acetylcholine-binding Protein (AChBP) from Aplysia californica in complex with an alpha-conotoxin PnIA variant
Components
  • ALPHA-CONOTOXIN PNIA
  • SOLUBLE ACETYLCHOLINE RECEPTOR
KeywordsRECEPTOR/INHIBITOR / RECEPTOR-INHIBITOR COMPLEX / GLYCOPROTEIN / IGG-FOLD / IMMUNOGLOBULIN DOMAIN / PENTAMER / NICOTINIC RECEPTOR / ALPHA-CONOTOXIN / RECEPTOR / ACETYLCHOLINE RECEPTOR INHIBITOR / AMIDATION / NEUROTOXIN / POSTSYNAPTIC NEUROTOXIN / SULFATION / TOXIN
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 / metal ion binding / identical protein binding / membrane
Similarity search - Function
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 PnIA / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAPLYSIA CALIFORNICA (California sea hare)
CONUS PENNACEUS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCelie, P.H.N. / Kasheverov, I.E. / Mordvintsev, D.Y. / Hogg, R.C. / van Nierop, P. / van Elk, R. / van Rossum-Fikkert, S.E. / Zhmak, M.N. / Bertrand, D. / Tsetlin, V. ...Celie, P.H.N. / Kasheverov, I.E. / Mordvintsev, D.Y. / Hogg, R.C. / van Nierop, P. / van Elk, R. / van Rossum-Fikkert, S.E. / Zhmak, M.N. / Bertrand, D. / Tsetlin, V. / Sixma, T.K. / Smit, A.B.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Crystal Structure of Nicotinic Acetylcholine Receptor Homolog Achbp in Complex with an Alpha-Conotoxin Pnia Variant
Authors: Celie, P.H.N. / Kasheverov, I.E. / Mordvintsev, D.Y. / Hogg, R.C. / Van Nierop, P. / Van Elk, R. / Van Rossum-Fikkert, S.E. / Zhmak, M.N. / Bertrand, D. / Tsetlin, V. / Sixma, T.K. / Smit, A.B.
History
DepositionMay 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2005Provider: 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 / 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_conn
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_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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: SOLUBLE ACETYLCHOLINE RECEPTOR
B: SOLUBLE ACETYLCHOLINE RECEPTOR
C: SOLUBLE ACETYLCHOLINE RECEPTOR
D: SOLUBLE ACETYLCHOLINE RECEPTOR
E: SOLUBLE ACETYLCHOLINE RECEPTOR
F: ALPHA-CONOTOXIN PNIA
G: ALPHA-CONOTOXIN PNIA
H: ALPHA-CONOTOXIN PNIA
I: ALPHA-CONOTOXIN PNIA
J: ALPHA-CONOTOXIN PNIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,33315
Polymers131,85310
Non-polymers4805
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.473, 80.085, 134.043
Angle α, β, γ (deg.)90.00, 93.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.98077, 0.03941, -0.19116), (-0.19343, 0.32701, -0.92501), (0.02606, 0.9442, 0.32834)4.57851, 99.5722, -53.47471
2given(0.95147, -0.13588, -0.27613), (-0.2745, -0.78037, -0.56184), (-0.13914, 0.61037, -0.7798)23.79596, 180.98698, 23.7221
3given(0.95434, -0.26896, -0.13), (-0.13747, -0.78176, 0.60823), (-0.26522, -0.56259, -0.78304)29.25271, 130.55984, 126.63183
4given(0.98519, -0.16998, 0.02263), (0.02916, 0.29611, 0.95471), (-0.16899, -0.93991, 0.29668)13.71913, 21.09977, 112.04836
5given(0.98597, 0.04183, -0.16158), (-0.16664, 0.30113, -0.93891), (0.00939, 0.95266, 0.30388)2.66594, 101.02425, -52.03304
6given(0.98364, -0.0273, -0.17804), (-0.12671, -0.8074, -0.57624), (-0.12802, 0.58938, -0.79765)6.1087, 173.67, 25.92109
7given(0.95762, -0.25351, -0.13673), (-0.09061, -0.71575, 0.69245), (-0.27341, -0.65072, -0.70839)27.82446, 116.21191, 133.62135
8given(0.9887, -0.08973, 0.12007), (-0.08667, 0.31135, 0.94633), (-0.1223, -0.94605, 0.30006)0.91302, 28.22668, 108.76913

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Components

#1: Protein
SOLUBLE ACETYLCHOLINE RECEPTOR / ACETYLCHOLINE-BINDING PROTEIN


Mass: 24688.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: HEPES BUFFER MOLECULE IDENTIFIED IN 4 OUT OF FIVE BINDING SITES
Source: (gene. exp.) APLYSIA CALIFORNICA (California sea hare)
Cell: GLIAL CELL / Plasmid: PFASTBACI / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q8WSF8
#2: Protein/peptide
ALPHA-CONOTOXIN PNIA / ALPHA-PNIA


Mass: 1682.021 Da / Num. of mol.: 5 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) CONUS PENNACEUS (invertebrata) / References: UniProt: P50984
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: ALPHA-CONOTOXINS INHIBIT THE NICOTINIC ACETYLCHOLINE RECEPTORS (NACHR) ENGINEERED RESIDUE ...FUNCTION: ALPHA-CONOTOXINS INHIBIT THE NICOTINIC ACETYLCHOLINE RECEPTORS (NACHR) ENGINEERED RESIDUE IN CHAIN F, ALA 10 TO LEU ENGINEERED RESIDUE IN CHAIN F, ASP 14 TO LYS ENGINEERED RESIDUE IN CHAIN G, ALA 10 TO LEU ENGINEERED RESIDUE IN CHAIN G, ASP 14 TO LYS ENGINEERED RESIDUE IN CHAIN H, ALA 10 TO LEU ENGINEERED RESIDUE IN CHAIN H, ASP 14 TO LYS ENGINEERED RESIDUE IN CHAIN I, ALA 10 TO LEU ENGINEERED RESIDUE IN CHAIN I, ASP 14 TO LYS ENGINEERED RESIDUE IN CHAIN J, ALA 10 TO LEU ENGINEERED RESIDUE IN CHAIN J, ASP 14 TO LYS
Has protein modificationY
Sequence detailsPROTEIN CONTAINS SIGNAL SEQUENCE MLVSVYLALLVACVGQAHS THAT IS CLEAVED UPON SECRETION AND IS NOT ...PROTEIN CONTAINS SIGNAL SEQUENCE MLVSVYLALLVACVGQAHS THAT IS CLEAVED UPON SECRETION AND IS NOT PRESENT IN PURIFIED PROTEIN. RESIDUES ARG206 - ASP217 IN CHAIN A,B,C,D,E ARE NOT VISUABLE IN THE STRUCTURE PNIA IN THIS STRUCTURE CONTAINS TWO MUTATIONS A10L AND D14K

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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: 2.9 Å3/Da / Density % sol: 57.5 %
Crystal growpH: 7.5
Details: 18 % PEG 3350, 180 MM NA2SO4, 100 MM BIS-TRIS PROPANE PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 55263 / % possible obs: 97.9 % / Observed criterion σ(I): 1.8 / Redundancy: 3.45 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6
Reflection shellResolution: 2.4→2.52 Å / Redundancy: 2.98 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.8 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UX2

1ux2


Resolution: 2.4→19.8 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 18.569 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2783 5.1 %RANDOM
Rwork0.198 ---
obs0.201 51866 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20.02 Å2
2--0.05 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8750 0 25 235 9010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229000
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.94612295
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20551095
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.05724.634410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.156151440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2451545
X-RAY DIFFRACTIONr_chiral_restr0.090.21370
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026865
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.23854
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25990
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2419
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4450.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4891.55727
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81129075
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.14833835
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8244.53220
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.365 172
Rwork0.296 3175

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