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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 / metal ion binding / identical protein binding / membrane
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
Revision 1.2Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _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

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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:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA20 - 22420 - 224
21ARGARGBB20 - 22420 - 224
12ARGARGAA20 - 22420 - 224
22ARGARGCC20 - 22420 - 224
13ARGARGAA20 - 22420 - 224
23ARGARGDD20 - 22420 - 224
14ARGARGAA20 - 22420 - 224
24ARGARGEE20 - 22420 - 224
15ARGARGAA20 - 22420 - 224
25ARGARGFF20 - 22420 - 224
16ARGARGAA20 - 22420 - 224
26ARGARGGG20 - 22420 - 224
17GLUGLUAA20 - 22320 - 223
27GLUGLUHH20 - 22320 - 223
18ARGARGAA20 - 22420 - 224
28ARGARGII20 - 22420 - 224
19ARGARGAA20 - 22420 - 224
29ARGARGJJ20 - 22420 - 224
110ARGARGBB20 - 22420 - 224
210ARGARGCC20 - 22420 - 224
111ARGARGBB20 - 22420 - 224
211ARGARGDD20 - 22420 - 224
112ARGARGBB20 - 22420 - 224
212ARGARGEE20 - 22420 - 224
113ARGARGBB20 - 22420 - 224
213ARGARGFF20 - 22420 - 224
114ARGARGBB20 - 22420 - 224
214ARGARGGG20 - 22420 - 224
115GLUGLUBB20 - 22320 - 223
215GLUGLUHH20 - 22320 - 223
116ARGARGBB20 - 22420 - 224
216ARGARGII20 - 22420 - 224
117ARGARGBB20 - 22420 - 224
217ARGARGJJ20 - 22420 - 224
118ARGARGCC20 - 22420 - 224
218ARGARGDD20 - 22420 - 224
119ARGARGCC20 - 22420 - 224
219ARGARGEE20 - 22420 - 224
120ARGARGCC20 - 22420 - 224
220ARGARGFF20 - 22420 - 224
121ARGARGCC20 - 22420 - 224
221ARGARGGG20 - 22420 - 224
122GLUGLUCC20 - 22320 - 223
222GLUGLUHH20 - 22320 - 223
123ARGARGCC20 - 22420 - 224
223ARGARGII20 - 22420 - 224
124ARGARGCC20 - 22420 - 224
224ARGARGJJ20 - 22420 - 224
125ARGARGDD20 - 22420 - 224
225ARGARGEE20 - 22420 - 224
126ARGARGDD20 - 22420 - 224
226ARGARGFF20 - 22420 - 224
127ARGARGDD20 - 22420 - 224
227ARGARGGG20 - 22420 - 224
128GLUGLUDD20 - 22320 - 223
228GLUGLUHH20 - 22320 - 223
129ARGARGDD20 - 22420 - 224
229ARGARGII20 - 22420 - 224
130ARGARGDD20 - 22420 - 224
230ARGARGJJ20 - 22420 - 224
131ARGARGEE20 - 22420 - 224
231ARGARGFF20 - 22420 - 224
132ARGARGEE20 - 22420 - 224
232ARGARGGG20 - 22420 - 224
133GLUGLUEE20 - 22320 - 223
233GLUGLUHH20 - 22320 - 223
134ARGARGEE20 - 22420 - 224
234ARGARGII20 - 22420 - 224
135ARGARGEE20 - 22420 - 224
235ARGARGJJ20 - 22420 - 224
136ARGARGFF20 - 22420 - 224
236ARGARGGG20 - 22420 - 224
137GLUGLUFF20 - 22320 - 223
237GLUGLUHH20 - 22320 - 223
138ARGARGFF20 - 22420 - 224
238ARGARGII20 - 22420 - 224
139ARGARGFF20 - 22420 - 224
239ARGARGJJ20 - 22420 - 224
140GLUGLUGG20 - 22320 - 223
240GLUGLUHH20 - 22320 - 223
141ARGARGGG20 - 22420 - 224
241ARGARGII20 - 22420 - 224
142ARGARGGG20 - 22420 - 224
242ARGARGJJ20 - 22420 - 224
143GLUGLUHH20 - 22320 - 223
243GLUGLUII20 - 22320 - 223
144GLUGLUHH20 - 22320 - 223
244GLUGLUJJ20 - 22320 - 223
145ARGARGII20 - 22420 - 224
245ARGARGJJ20 - 22420 - 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


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


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


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

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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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