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- PDB-4xhe: Crystal Structure of A-AChBP in complex with pinnatoxin A -

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Basic information

Entry
Database: PDB / ID: 4xhe
TitleCrystal Structure of A-AChBP in complex with pinnatoxin A
ComponentsSoluble acetylcholine receptor
KeywordsACETYLCHOLINE-BINDING PROTEIN / receptor / phycotoxin / pinnatoxin / membrane protein
Function / homology
Function and homology information


acetylcholine receptor activity / acetylcholine-gated monoatomic cation-selective channel activity / response to nicotine / postsynapse / neuron projection / 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
Pinnatoxin A / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBourne, Y. / Sulzenbacher, G. / Marchot, P.
CitationJournal: Structure / Year: 2015
Title: Marine Macrocyclic Imines, Pinnatoxins A and G: Structural Determinants and Functional Properties to Distinguish Neuronal alpha 7 from Muscle alpha 12 beta gamma delta nAChRs.
Authors: Bourne, Y. / Sulzenbacher, G. / Radic, Z. / Araoz, R. / Reynaud, M. / Benoit, E. / Zakarian, A. / Servent, D. / Molgo, J. / Taylor, P. / Marchot, P.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)254,58525
Polymers247,27510
Non-polymers7,31015
Water33,1661841
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)127,31313
Polymers123,6375
Non-polymers3,6758
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15330 Å2
ΔGint-90 kcal/mol
Surface area44760 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)127,27312
Polymers123,6375
Non-polymers3,6357
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-81 kcal/mol
Surface area43570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.734, 144.231, 147.121
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 24727.484 Da / Num. of mol.: 10 / Fragment: UNP residues 18-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-40P / Pinnatoxin A


Mass: 711.924 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C41H61NO9
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1841 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% (w/v) P400, 0.1M Hepes pH 7.5, 0.2M CaCl2, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→73 Å / Num. obs: 211460 / % possible obs: 98 % / Redundancy: 4.1 % / Rsym value: 0.093 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.7 / % possible all: 96.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.15data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BYN

2byn


Resolution: 1.9→64.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.642 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.216 6419 3 %RANDOM
Rwork0.1734 204994 --
obs0.1747 204994 97.65 %-
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 max: 89.99 Å2 / Biso mean: 28.416 Å2 / Biso min: 9.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å2-0 Å2-0 Å2
2---0.53 Å20 Å2
3----1.06 Å2
Refinement stepCycle: final / Resolution: 1.9→64.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16880 0 515 1841 19236
Biso mean--19.89 30.17 -
Num. residues----2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02218354
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212379
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9925263
X-RAY DIFFRACTIONr_angle_other_deg0.8253.00130282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40652244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70924.286861
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.129152963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.91615115
X-RAY DIFFRACTIONr_chiral_restr0.130.22841
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02120093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023666
X-RAY DIFFRACTIONr_mcbond_it1.435310822
X-RAY DIFFRACTIONr_mcbond_other0.43234254
X-RAY DIFFRACTIONr_mcangle_it2.283417770
X-RAY DIFFRACTIONr_scbond_it1.67837532
X-RAY DIFFRACTIONr_scangle_it2.48747422
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 482 -
Rwork0.248 14752 -
all-15234 -
obs--96.02 %
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)
10.2442-0.02670.10970.70630.1880.66990.0104-0.0428-0.02050.0756-0.04760.060.0546-0.10360.03720.0114-0.01780.00590.05880.00780.0555-2.975-22.10948.577
20.48310.12290.2740.3912-0.0880.83190.0124-0.0491-0.0125-0.01150.00060.01990.1867-0.0546-0.0130.0519-0.00950.00040.0080.00340.057-5.463-37.60326.957
30.2251-0.10880.16850.5748-0.10990.61260.04130.0211-0.0285-0.059-0.05740.01980.00690.0020.01610.0260.01630.00510.0298-0.01610.0373-6.808-21.7685.409
40.3586-0.08730.19770.35360.22031.004-0.04070.0130.0263-0.0506-0.0495-0.0038-0.2127-0.05810.09020.07370.0143-0.01370.00890.00220.0381-6.3193.79913.568
50.2458-0.03370.03050.48-0.23490.7688-0.0362-0.06030.00650.03910.02460.0237-0.1537-0.07670.01160.04540.0145-0.01550.0434-0.01860.0511-4.3594.00340.461
60.18230.1929-0.03220.47320.11380.96320.0192-0.03710.00170.0761-0.04260.00460.0672-0.01630.02340.01910.003600.03430.00680.0407-68.009-6.01548.744
70.42120.10870.15030.5004-0.1441.11330.0078-0.0244-0.0105-0.03180.00360.02710.2346-0.0639-0.01140.0691-0.00210.00610.0109-0.00020.053-70.471-21.54527.189
80.50780.0855-0.06320.8328-0.24970.69220.02530.06060.0091-0.0906-0.01630.07430.0967-0.0389-0.0090.03340.0185-0.00030.044-0.00930.032-71.587-5.9015.207
90.47090.03990.10260.28430.13071.14150.01220.03890.0437-0.0351-0.03-0.0096-0.159-0.0640.01780.0290.01630.01260.01280.01260.0398-69.4819.31813.155
100.21860.0064-0.15760.3901-0.21881.0125-0.00720.0031-0.00460.0760.0116-0.0228-0.1464-0.0255-0.00440.03160.0043-0.00360.0137-0.01880.0385-67.96719.52540.397
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-7 - 208
2X-RAY DIFFRACTION2B-8 - 208
3X-RAY DIFFRACTION3C-2 - 208
4X-RAY DIFFRACTION4D-2 - 208
5X-RAY DIFFRACTION5E-2 - 208
6X-RAY DIFFRACTION6F-4 - 208
7X-RAY DIFFRACTION7G-2 - 207
8X-RAY DIFFRACTION8H-3 - 208
9X-RAY DIFFRACTION9I0 - 207
10X-RAY DIFFRACTION10J-2 - 208

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