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- PDB-6sgv: Crystal structure of AcAChBP in complex with hosieine -

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Basic information

Entry
Database: PDB / ID: 6sgv
TitleCrystal structure of AcAChBP in complex with hosieine
ComponentsSoluble acetylcholine receptor
KeywordsSIGNALING PROTEIN / toxin / acetylcholine binding protein
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
ACETATE ION / Hosieine / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsHunter, W.N. / Dawson, A. / Parker, H.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Delineating the activity of the potent nicotinic acetylcholine receptor agonists (+)-anatoxin-a and (-)-hosieine-A
Authors: Parker, H.P. / Dawson, A. / Jones, M.J. / Yan, R. / Ouyang, J. / Hong, R. / Hunter, W.N.
History
DepositionAug 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)286,43324
Polymers283,26810
Non-polymers3,16614
Water7,819434
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)143,51913
Polymers141,6345
Non-polymers1,8858
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14110 Å2
ΔGint-60 kcal/mol
Surface area42150 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)142,91411
Polymers141,6345
Non-polymers1,2816
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-69 kcal/mol
Surface area41710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.802, 133.414, 131.155
Angle α, β, γ (deg.)90.000, 102.510, 90.000
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A20 - 224
2010B20 - 224
1020A20 - 224
2020C20 - 224
1030A20 - 224
2030D20 - 224
1040A20 - 224
2040E20 - 224
1050A20 - 224
2050F20 - 224
1060A20 - 224
2060G20 - 224
1070A20 - 223
2070H20 - 223
1080A20 - 224
2080I20 - 224
1090A20 - 224
2090J20 - 224
10100B20 - 224
20100C20 - 224
10110B20 - 224
20110D20 - 224
10120B20 - 224
20120E20 - 224
10130B20 - 224
20130F20 - 224
10140B20 - 224
20140G20 - 224
10150B20 - 223
20150H20 - 223
10160B20 - 224
20160I20 - 224
10170B20 - 224
20170J20 - 224
10180C20 - 224
20180D20 - 224
10190C20 - 224
20190E20 - 224
10200C20 - 224
20200F20 - 224
10210C20 - 224
20210G20 - 224
10220C20 - 223
20220H20 - 223
10230C20 - 224
20230I20 - 224
10240C20 - 224
20240J20 - 224
10250D20 - 224
20250E20 - 224
10260D20 - 224
20260F20 - 224
10270D20 - 224
20270G20 - 224
10280D20 - 223
20280H20 - 223
10290D20 - 224
20290I20 - 224
10300D20 - 224
20300J20 - 224
10310E20 - 224
20310F20 - 224
10320E20 - 224
20320G20 - 224
10330E20 - 223
20330H20 - 223
10340E20 - 224
20340I20 - 224
10350E20 - 224
20350J20 - 224
10360F20 - 224
20360G20 - 224
10370F20 - 223
20370H20 - 223
10380F20 - 224
20380I20 - 224
10390F20 - 224
20390J20 - 224
10400G20 - 223
20400H20 - 223
10410G20 - 224
20410I20 - 224
10420G20 - 224
20420J20 - 224
10430H20 - 223
20430I20 - 223
10440H20 - 223
20440J20 - 223
10450I20 - 224
20450J20 - 224

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: 28326.750 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8
#2: 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.: 3
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
#3: Chemical
ChemComp-LDQ / Hosieine


Mass: 244.332 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C15H20N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.84 Å3/Da / Density % sol: 68 % / Description: prism
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: reservoir solution: 0.2 M CaCl2, 0.1M NaOAc pH 4.5, 16% isopropanol Protein buffer: 50 mM tris pH 7.5, 250 mM NaCl, 4 mg/ml mixed in 1ul protein : 2 ul reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 19, 2018
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→45.03 Å / Num. obs: 108313 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.5 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.104 / Rrim(I) all: 0.261 / Net I/σ(I): 6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.96 / Num. unique obs: 5354 / CC1/2: 0.776 / Rpim(I) all: 0.418 / Rrim(I) all: 1.048 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.03 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.889 / SU B: 9.588 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.277
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 5457 5 %RANDOM
Rwork0.2323 ---
obs0.2335 102825 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.85 Å2 / Biso mean: 28.07 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å2-0.86 Å2
2--2.94 Å20 Å2
3----0.89 Å2
Refinement stepCycle: final / Resolution: 2.6→45.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16371 0 226 434 17031
Biso mean--32.63 19.88 -
Num. residues----2051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0217109
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215191
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9523408
X-RAY DIFFRACTIONr_angle_other_deg0.938335395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02652051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6524.411798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.498152744
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7571598
X-RAY DIFFRACTIONr_chiral_restr0.0840.22648
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023472
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A129960.04
12B129960.04
21A130340.03
22C130340.03
31A130080.03
32D130080.03
41A130080.04
42E130080.04
51A129980.03
52F129980.03
61A129440.04
62G129440.04
71A129060.04
72H129060.04
81A129960.04
82I129960.04
91A129900.04
92J129900.04
101B130580.03
102C130580.03
111B130560.04
112D130560.04
121B130460.03
122E130460.03
131B128940.04
132F128940.04
141B130560.02
142G130560.02
151B129340.03
152H129340.03
161B130120.04
162I130120.04
171B130260.03
172J130260.03
181C131240.03
182D131240.03
191C131260.03
192E131260.03
201C129900.04
202F129900.04
211C130340.04
212G130340.04
221C130340.03
222H130340.03
231C130600.04
232I130600.04
241C131060.03
242J131060.03
251D131260.04
252E131260.04
261D130220.04
262F130220.04
271D130860.04
272G130860.04
281D130000.03
282H130000.03
291D131380.03
292I131380.03
301D131000.04
302J131000.04
311E129380.04
312F129380.04
321E130120.04
322G130120.04
331E129820.03
332H129820.03
341E130300.04
342I130300.04
351E130780.03
352J130780.03
361F129060.05
362G129060.05
371F129020.04
372H129020.04
381F129320.05
382I129320.05
391F129580.04
392J129580.04
401G128640.04
402H128640.04
411G129600.04
412I129600.04
421G129700.03
422J129700.03
431H129760.04
432I129760.04
441H129660.03
442J129660.03
451I130540.04
452J130540.04
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 407 -
Rwork0.291 7547 -
all-7954 -
obs--99.94 %

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