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- PDB-4xk9: Crystal structure of A-AChBP in complex with pinnatoxin G -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4xk9
TitleCrystal structure of A-AChBP in complex with pinnatoxin G
ComponentsSoluble acetylcholine receptor
KeywordsACETYLCHOLINE-BINDING PROTEIN / receptor / phycotoxin
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / 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 G / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 10, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)266,86627
Polymers259,67810
Non-polymers7,18817
Water16,718928
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)133,45114
Polymers129,8395
Non-polymers3,6129
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15230 Å2
ΔGint-112 kcal/mol
Surface area43450 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)133,41513
Polymers129,8395
Non-polymers3,5768
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15560 Å2
ΔGint-95 kcal/mol
Surface area43580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.844, 142.918, 142.130
Angle α, β, γ (deg.)90.00, 126.48, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: _ / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSAA-1 - 2078 - 216
21LYSLYSBB-1 - 2078 - 216
12HISHISAA1 - 20710 - 216
22HISHISCC1 - 20710 - 216
13SERSERAA2 - 20711 - 216
23SERSERDD2 - 20711 - 216
14LEULEUAA0 - 2079 - 216
24LEULEUEE0 - 2079 - 216
15LYSLYSAA-1 - 2078 - 216
25LYSLYSFF-1 - 2078 - 216
16HISHISAA1 - 20710 - 216
26HISHISGG1 - 20710 - 216
17LEULEUAA0 - 2079 - 216
27LEULEUHH0 - 2079 - 216
18LYSLYSAA-1 - 2078 - 216
28LYSLYSII-1 - 2078 - 216
19LEULEUAA0 - 2079 - 216
29LEULEUJJ0 - 2079 - 216
110HISHISBB1 - 20710 - 216
210HISHISCC1 - 20710 - 216
111SERSERBB2 - 20711 - 216
211SERSERDD2 - 20711 - 216
112ASPASPBB-3 - 2076 - 216
212ASPASPEE-3 - 2076 - 216
113ASPASPBB-2 - 2077 - 216
213ASPASPFF-2 - 2077 - 216
114HISHISBB1 - 20710 - 216
214HISHISGG1 - 20710 - 216
115ASPASPBB-3 - 2076 - 216
215ASPASPHH-3 - 2076 - 216
116ASPASPBB-2 - 2077 - 216
216ASPASPII-2 - 2077 - 216
117ASPASPBB-3 - 2076 - 216
217ASPASPJJ-3 - 2076 - 216
118SERSERCC2 - 20711 - 216
218SERSERDD2 - 20711 - 216
119HISHISCC1 - 20710 - 216
219HISHISEE1 - 20710 - 216
120LEULEUCC0 - 2079 - 216
220LEULEUFF0 - 2079 - 216
121HISHISCC1 - 20710 - 216
221HISHISGG1 - 20710 - 216
122HISHISCC1 - 20710 - 216
222HISHISHH1 - 20710 - 216
123LEULEUCC0 - 2079 - 216
223LEULEUII0 - 2079 - 216
124HISHISCC1 - 20710 - 216
224HISHISJJ1 - 20710 - 216
125SERSERDD2 - 20711 - 216
225SERSEREE2 - 20711 - 216
126SERSERDD2 - 20711 - 216
226SERSERFF2 - 20711 - 216
127SERSERDD2 - 20711 - 216
227SERSERGG2 - 20711 - 216
128SERSERDD2 - 20711 - 216
228SERSERHH2 - 20711 - 216
129SERSERDD2 - 20711 - 216
229SERSERII2 - 20711 - 216
130SERSERDD2 - 20711 - 216
230SERSERJJ2 - 20711 - 216
131ASPASPEE-2 - 2077 - 216
231ASPASPFF-2 - 2077 - 216
132HISHISEE1 - 20710 - 216
232HISHISGG1 - 20710 - 216
133ASPASPEE-3 - 2086 - 217
233ASPASPHH-3 - 2086 - 217
134ASPASPEE-2 - 2077 - 216
234ASPASPII-2 - 2077 - 216
135ASPASPEE-3 - 2086 - 217
235ASPASPJJ-3 - 2086 - 217
136HISHISFF1 - 20710 - 216
236HISHISGG1 - 20710 - 216
137ASPASPFF-2 - 2077 - 216
237ASPASPHH-2 - 2077 - 216
138ASPASPFF-2 - 2087 - 217
238ASPASPII-2 - 2087 - 217
139ASPASPFF-2 - 2077 - 216
239ASPASPJJ-2 - 2077 - 216
140HISHISGG1 - 20710 - 216
240HISHISHH1 - 20710 - 216
141HISHISGG1 - 20710 - 216
241HISHISII1 - 20710 - 216
142HISHISGG1 - 20710 - 216
242HISHISJJ1 - 20710 - 216
143ASPASPHH-2 - 2077 - 216
243ASPASPII-2 - 2077 - 216
144ASPASPHH-3 - 2086 - 217
244ASPASPJJ-3 - 2086 - 217
145ASPASPII-2 - 2077 - 216
245ASPASPJJ-2 - 2077 - 216

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

#1: Protein
Soluble acetylcholine receptor


Mass: 25967.832 Da / Num. of mol.: 10 / Fragment: UNP residues 18-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Plasmid: pCDNA 3.1 / Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human) / References: UniProt: Q8WSF8
#2: Chemical
ChemComp-41J / Pinnatoxin G


Mass: 693.952 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C42H63NO7
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / 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

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 8% (w/v) P4000, 0.1M Hepes pH 7.5, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.2→34 Å / Num. all: 149555 / Num. obs: 149555 / % possible obs: 99.6 % / Redundancy: 3.8 % / Rsym value: 0.074 / Net I/σ(I): 9.8 / Num. measured all: 441534
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BYN
Resolution: 2.2→34 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.941 / SU B: 10.517 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21135 7513 5 %RANDOM
Rwork0.19907 ---
obs0.1997 142034 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.974 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.06 Å2
2---0.43 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16745 0 507 928 18180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217844
X-RAY DIFFRACTIONr_bond_other_d0.0070.0216352
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.98924489
X-RAY DIFFRACTIONr_angle_other_deg1.424337790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43152119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66324.263821
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.014152809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.84915106
X-RAY DIFFRACTIONr_chiral_restr0.0750.22766
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119787
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024047
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0472.6028434
X-RAY DIFFRACTIONr_mcbond_other1.0472.6028433
X-RAY DIFFRACTIONr_mcangle_it1.8853.89410531
X-RAY DIFFRACTIONr_mcangle_other1.8853.89410532
X-RAY DIFFRACTIONr_scbond_it1.0142.7179406
X-RAY DIFFRACTIONr_scbond_other1.0142.7179407
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7294.01813944
X-RAY DIFFRACTIONr_long_range_B_refined4.51220.77319715
X-RAY DIFFRACTIONr_long_range_B_other4.43220.5619403
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A238180.07
12B238180.07
21A235820.07
22C235820.07
31A235180.07
32D235180.07
41A238300.06
42E238300.06
51A241680.05
52F241680.05
61A235800.08
62G235800.08
71A236560.07
72H236560.07
81A240140.06
82I240140.06
91A238600.06
92J238600.06
101B234340.07
102C234340.07
111B235880.08
112D235880.08
121B238860.08
122E238860.08
131B239100.07
132F239100.07
141B238440.07
142G238440.07
151B237760.08
152H237760.08
161B239620.08
162I239620.08
171B241360.07
172J241360.07
181C232880.09
182D232880.09
191C236440.07
192E236440.07
201C236380.07
202F236380.07
211C234900.07
212G234900.07
221C240280.05
222H240280.05
231C235160.08
232I235160.08
241C237440.07
242J237440.07
251D234400.08
252E234400.08
261D235100.07
262F235100.07
271D234180.09
272G234180.09
281D231060.09
282H231060.09
291D238460.06
292I238460.06
301D234440.08
302J234440.08
311E237520.07
312F237520.07
321E237200.07
322G237200.07
331E241320.07
332H241320.07
341E238340.08
342I238340.08
351E245900.05
352J245900.05
361F236200.08
362G236200.08
371F238860.08
372H238860.08
381F240500.07
382I240500.07
391F239020.07
392J239020.07
401G234940.08
402H234940.08
411G236160.08
412I236160.08
421G238900.06
422J238900.06
431H237880.08
432I237880.08
441H242560.06
442J242560.06
451I240380.08
452J240380.08
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 525 -
Rwork0.319 10438 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9259-0.2230.16971.507-0.13360.7568-0.08090.00590.09490.1324-0.0067-0.2338-0.12120.05050.08760.0625-0.0157-0.03960.06860.03140.055869.951611.264721.6112
21.08280.0794-0.21871.0283-0.39641.3845-0.0727-0.02240.07110.0826-0.0198-0.0809-0.1908-0.00340.09250.10360.0213-0.03260.01190.00910.048457.818631.09477.9479
30.43560.18820.00641.34390.00990.7317-0.0521-0.01820.0241-0.26630.05130.161-0.0308-0.07670.00080.10720.033-0.03710.05310.02730.069741.813520.4174-10.4409
40.8063-0.16080.13311.3705-0.02951.22320.06640.0277-0.0471-0.30120.03990.16030.0741-0.0519-0.10630.1034-0.0256-0.06240.0260.02530.045143.922-6.2625-9.1196
51.0260.05330.19570.70860.08851.07280.02710.0225-0.09060.02360.045-0.07860.13990.0475-0.07210.046-0.0023-0.01210.03190.02260.056862.2114-11.713610.434
61.19890.1421-0.26621.7122-0.05080.95040.04880.04240.0207-0.29530.02170.32930.0643-0.0976-0.07050.078-0.0071-0.07190.06070.02590.078864.066235.7472-78.5374
70.67750.02060.32731.028-0.05131.3942-0.0243-0.06620.0734-0.00970.0280.0858-0.1573-0.05-0.00370.0598-0.01620.00920.03890.02190.0674.673556.2521-65.5177
80.4839-0.1543-0.01111.0432-0.23270.92620.0211-0.04990.03940.1723-0.0095-0.1434-0.05860.1512-0.01160.065-0.0523-0.01420.0932-0.00260.066191.170146.2036-46.2793
90.6060.3129-0.01041.5160.10961.04680.0377-0.08-0.10040.2502-0.0282-0.19630.10530.1228-0.00950.07890.0593-0.02230.11520.03120.073390.603419.5628-47.8485
100.82530.02170.36980.9482-0.11870.7884-0.0092-0.0468-0.0515-0.18090.03890.10490.18020.025-0.02980.09850.0263-0.00750.03020.00410.070873.546813.1532-67.6133
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 208
2X-RAY DIFFRACTION2B-4 - 208
3X-RAY DIFFRACTION3C0 - 208
4X-RAY DIFFRACTION4D2 - 208
5X-RAY DIFFRACTION5E-3 - 208
6X-RAY DIFFRACTION6F-2 - 208
7X-RAY DIFFRACTION7G1 - 208
8X-RAY DIFFRACTION8H-3 - 208
9X-RAY DIFFRACTION9I-2 - 208
10X-RAY DIFFRACTION10J-3 - 208

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