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- PDB-5oaj: Crystal structure of mutant AChBP in complex with tropisetron (T5... -

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Basic information

Entry
Database: PDB / ID: 5oaj
TitleCrystal structure of mutant AChBP in complex with tropisetron (T53F, Q74R, Y110A, I135S, G162E)
ComponentsSoluble acetylcholine receptor
KeywordsSIGNALING PROTEIN / receptor / acetylcholine binding
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
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
CITRATE ANION / Chem-TKT / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsDawson, A. / Hunter, W.N. / de Souza, J.O. / Trumper, P.
CitationJournal: Iucrj / Year: 2019
Title: Engineering a surrogate human heteromeric alpha / beta glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein.
Authors: Dawson, A. / Trumper, P. / de Souza, J.O. / Parker, H. / Jones, M.J. / Hales, T.G. / Hunter, W.N.
History
DepositionJun 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source / Item: _diffrn_source.pdbx_wavelength_list
Revision 1.2Feb 12, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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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)288,18561
Polymers283,55810
Non-polymers4,62851
Water9,746541
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)143,93629
Polymers141,7795
Non-polymers2,15724
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19290 Å2
ΔGint-6 kcal/mol
Surface area42720 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)144,24932
Polymers141,7795
Non-polymers2,47027
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19690 Å2
ΔGint6 kcal/mol
Surface area42230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.239, 137.469, 103.666
Angle α, β, γ (deg.)90.00, 90.79, 90.00
Int Tables number4
Space group name H-MP1211
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: 0 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA20 - 22420 - 224
21ARGARGBB20 - 22420 - 224
12GLUGLUAA20 - 22320 - 223
22GLUGLUCC20 - 22320 - 223
13ARGARGAA20 - 22520 - 225
23ARGARGDD20 - 22520 - 225
14ARGARGAA20 - 22520 - 225
24ARGARGEE20 - 22520 - 225
15ARGARGAA20 - 22520 - 225
25ARGARGFF20 - 22520 - 225
16GLUGLUAA20 - 22320 - 223
26GLUGLUGG20 - 22320 - 223
17ARGARGAA20 - 22520 - 225
27ARGARGHH20 - 22520 - 225
18ARGARGAA20 - 22520 - 225
28ARGARGII20 - 22520 - 225
19ARGARGAA20 - 22420 - 224
29ARGARGJJ20 - 22420 - 224
110GLUGLUBB20 - 22320 - 223
210GLUGLUCC20 - 22320 - 223
111ARGARGBB20 - 22420 - 224
211ARGARGDD20 - 22420 - 224
112ARGARGBB20 - 22420 - 224
212ARGARGEE20 - 22420 - 224
113ARGARGBB20 - 22420 - 224
213ARGARGFF20 - 22420 - 224
114GLUGLUBB20 - 22320 - 223
214GLUGLUGG20 - 22320 - 223
115ARGARGBB20 - 22420 - 224
215ARGARGHH20 - 22420 - 224
116ARGARGBB20 - 22420 - 224
216ARGARGII20 - 22420 - 224
117TYRTYRBB20 - 24020 - 240
217TYRTYRJJ20 - 24020 - 240
118GLUGLUCC20 - 22320 - 223
218GLUGLUDD20 - 22320 - 223
119GLUGLUCC20 - 22320 - 223
219GLUGLUEE20 - 22320 - 223
120GLUGLUCC20 - 22320 - 223
220GLUGLUFF20 - 22320 - 223
121ARGARGCC20 - 22420 - 224
221ARGARGGG20 - 22420 - 224
122GLUGLUCC20 - 22320 - 223
222GLUGLUHH20 - 22320 - 223
123GLUGLUCC20 - 22320 - 223
223GLUGLUII20 - 22320 - 223
124GLUGLUCC20 - 22320 - 223
224GLUGLUJJ20 - 22320 - 223
125ARGARGDD20 - 22520 - 225
225ARGARGEE20 - 22520 - 225
126ARGARGDD20 - 22520 - 225
226ARGARGFF20 - 22520 - 225
127GLUGLUDD20 - 22320 - 223
227GLUGLUGG20 - 22320 - 223
128ARGARGDD20 - 22520 - 225
228ARGARGHH20 - 22520 - 225
129ARGARGDD20 - 22520 - 225
229ARGARGII20 - 22520 - 225
130ARGARGDD20 - 22420 - 224
230ARGARGJJ20 - 22420 - 224
131ARGARGEE20 - 22520 - 225
231ARGARGFF20 - 22520 - 225
132GLUGLUEE20 - 22320 - 223
232GLUGLUGG20 - 22320 - 223
133ARGARGEE20 - 22520 - 225
233ARGARGHH20 - 22520 - 225
134ARGARGEE20 - 22520 - 225
234ARGARGII20 - 22520 - 225
135ARGARGEE20 - 22420 - 224
235ARGARGJJ20 - 22420 - 224
136GLUGLUFF20 - 22320 - 223
236GLUGLUGG20 - 22320 - 223
137ARGARGFF20 - 22520 - 225
237ARGARGHH20 - 22520 - 225
138ARGARGFF20 - 22520 - 225
238ARGARGII20 - 22520 - 225
139ARGARGFF20 - 22420 - 224
239ARGARGJJ20 - 22420 - 224
140GLUGLUGG20 - 22320 - 223
240GLUGLUHH20 - 22320 - 223
141GLUGLUGG20 - 22320 - 223
241GLUGLUII20 - 22320 - 223
142GLUGLUGG20 - 22320 - 223
242GLUGLUJJ20 - 22320 - 223
143ARGARGHH20 - 22520 - 225
243ARGARGII20 - 22520 - 225
144ARGARGHH20 - 22420 - 224
244ARGARGJJ20 - 22420 - 224
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

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Protein / Sugars , 2 types, 14 molecules ABCDEFGHIJ

#1: Protein
Soluble acetylcholine receptor


Mass: 28355.773 Da / Num. of mol.: 10 / Mutation: T53F, Q74R, Y110A, I135S, G162E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aplysia californica (California sea hare)
Production host: Spodoptera frugiperda (fall armyworm) / Variant (production host): Sf9 / 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.: 4
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

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Non-polymers , 4 types, 588 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-TKT / (3-ENDO)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL 1H-INDOLE-3-CARBOXYLATE / TROPISETRON / Tropisetron


Mass: 284.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: chemotherapy, antagonist*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Reservoir condition: 20% PEG3350, 0.2 M Na citrate. Protein buffer: 50 mM tris, 250 mM NaCl, pH 7.5, 5 mM tropisetron

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91739 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91739 Å / Relative weight: 1
ReflectionResolution: 2.47→42.66 Å / Num. obs: 97730 / % possible obs: 97.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.3 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.2
Reflection shellResolution: 2.47→2.51 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 4799 / CC1/2: 0.854 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xys
Resolution: 2.47→42.66 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20781 4738 4.8 %RANDOM
Rwork0.17284 ---
obs0.17457 92964 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.005 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20.93 Å2
2--1.34 Å20 Å2
3----1.14 Å2
Refinement stepCycle: 1 / Resolution: 2.47→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16662 0 305 541 17508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0217408
X-RAY DIFFRACTIONr_bond_other_d00.0215483
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.95823667
X-RAY DIFFRACTIONr_angle_other_deg3.752336014
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1135.0382081
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47324.248824
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.646152782
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.68715108
X-RAY DIFFRACTIONr_chiral_restr0.1090.22625
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02119296
X-RAY DIFFRACTIONr_gen_planes_other0.0280.023568
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_it4.0313.7358334
X-RAY DIFFRACTIONr_mcbond_other4.0283.7358333
X-RAY DIFFRACTIONr_mcangle_it5.7015.59410397
X-RAY DIFFRACTIONr_mcangle_other5.7025.59510398
X-RAY DIFFRACTIONr_scbond_it5.654.3259074
X-RAY DIFFRACTIONr_scbond_other5.6484.3259074
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2036.24813270
X-RAY DIFFRACTIONr_long_range_B_refined9.77843.30618695
X-RAY DIFFRACTIONr_long_range_B_other9.78243.28618656
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)
11A130720.05
12B130720.05
21A130580.04
22C130580.04
31A132080.04
32D132080.04
41A131360.05
42E131360.05
51A131240.05
52F131240.05
61A130560.04
62G130560.04
71A132420.04
72H132420.04
81A132440.04
82I132440.04
91A130500.06
92J130500.06
101B130300.04
102C130300.04
111B131180.04
112D131180.04
121B129900.06
122E129900.06
131B130840.04
132F130840.04
141B130400.04
142G130400.04
151B130820.04
152H130820.04
161B131260.04
162I131260.04
171B133060.07
172J133060.07
181C130600.04
182D130600.04
191C129560.06
192E129560.06
201C130020.04
202F130020.04
211C131620.05
212G131620.05
221C130240.05
222H130240.05
231C130440.04
232I130440.04
241C130000.06
242J130000.06
251D131440.05
252E131440.05
261D131620.04
262F131620.04
271D131140.04
272G131140.04
281D132400.04
282H132400.04
291D131920.04
292I131920.04
301D131480.05
302J131480.05
311E131940.05
312F131940.05
321E129760.06
322G129760.06
331E132980.05
332H132980.05
341E131540.06
342I131540.06
351E130320.07
352J130320.07
361F129740.05
362G129740.05
371F132400.04
372H132400.04
381F131660.04
382I131660.04
391F130320.05
392J130320.05
401G128840.04
402H128840.04
411G129840.03
412I129840.03
421G128980.06
422J128980.06
431H131820.04
432I131820.04
441H130920.05
442J130920.05
451I130900.05
452J130900.05
LS refinement shellResolution: 2.469→2.533 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 355 -
Rwork0.233 6845 -
obs--97.49 %

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