[English] 日本語
Yorodumi
- PDB-5o87: Crystal structure of wild type Aplysia californica AChBP in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5o87
TitleCrystal structure of wild type Aplysia californica AChBP in complex with nicotine
ComponentsSoluble acetylcholine receptor
KeywordsSIGNALING PROTEIN / receptor
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
ISOPROPYL ALCOHOL / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / PHOSPHATE ION / Soluble acetylcholine receptor
Similarity search - Component
Biological speciesAplysia californica (California sea hare)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDawson, A. / Hunter, W.N. / de Souza, J.O. / Trumper, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
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 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 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 1.2Jul 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 / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)292,209102
Polymers283,26810
Non-polymers8,94292
Water32,4451801
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)146,16752
Polymers141,6345
Non-polymers4,53347
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26140 Å2
ΔGint16 kcal/mol
Surface area39890 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)146,04250
Polymers141,6345
Non-polymers4,40945
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25530 Å2
ΔGint2 kcal/mol
Surface area39590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.781, 131.999, 130.655
Angle α, β, γ (deg.)90.00, 103.15, 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: 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
12ARGARGAA20 - 22520 - 225
22ARGARGCC20 - 22520 - 225
13ARGARGAA20 - 22520 - 225
23ARGARGDD20 - 22520 - 225
14ARGARGAA20 - 22520 - 225
24ARGARGEE20 - 22520 - 225
15ARGARGAA20 - 22520 - 225
25ARGARGFF20 - 22520 - 225
16ARGARGAA20 - 22520 - 225
26ARGARGGG20 - 22520 - 225
17GLUGLUAA20 - 22320 - 223
27GLUGLUHH20 - 22320 - 223
18ARGARGAA20 - 22520 - 225
28ARGARGII20 - 22520 - 225
19ARGARGAA20 - 22520 - 225
29ARGARGJJ20 - 22520 - 225
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 - 22520 - 225
218ARGARGDD20 - 22520 - 225
119ARGARGCC20 - 22520 - 225
219ARGARGEE20 - 22520 - 225
120ARGARGCC20 - 22520 - 225
220ARGARGFF20 - 22520 - 225
121ARGARGCC20 - 22520 - 225
221ARGARGGG20 - 22520 - 225
122GLUGLUCC20 - 22320 - 223
222GLUGLUHH20 - 22320 - 223
123ARGARGCC20 - 22520 - 225
223ARGARGII20 - 22520 - 225
124ARGARGCC20 - 22520 - 225
224ARGARGJJ20 - 22520 - 225
125ARGARGDD20 - 22520 - 225
225ARGARGEE20 - 22520 - 225
126ARGARGDD20 - 22520 - 225
226ARGARGFF20 - 22520 - 225
127ARGARGDD20 - 22520 - 225
227ARGARGGG20 - 22520 - 225
128GLUGLUDD20 - 22320 - 223
228GLUGLUHH20 - 22320 - 223
129ARGARGDD20 - 22520 - 225
229ARGARGII20 - 22520 - 225
130ARGARGDD20 - 22520 - 225
230ARGARGJJ20 - 22520 - 225
131ARGARGEE20 - 22520 - 225
231ARGARGFF20 - 22520 - 225
132ARGARGEE20 - 22520 - 225
232ARGARGGG20 - 22520 - 225
133GLUGLUEE20 - 22320 - 223
233GLUGLUHH20 - 22320 - 223
134ARGARGEE20 - 22520 - 225
234ARGARGII20 - 22520 - 225
135ARGARGEE20 - 22520 - 225
235ARGARGJJ20 - 22520 - 225
136ARGARGFF20 - 22520 - 225
236ARGARGGG20 - 22520 - 225
137GLUGLUFF20 - 22320 - 223
237GLUGLUHH20 - 22320 - 223
138ARGARGFF20 - 22520 - 225
238ARGARGII20 - 22520 - 225
139ARGARGFF20 - 22520 - 225
239ARGARGJJ20 - 22520 - 225
140GLUGLUGG20 - 22320 - 223
240GLUGLUHH20 - 22320 - 223
141ARGARGGG20 - 22520 - 225
241ARGARGII20 - 22520 - 225
142ARGARGGG20 - 22520 - 225
242ARGARGJJ20 - 22520 - 225
143GLUGLUHH20 - 22320 - 223
243GLUGLUII20 - 22320 - 223
144GLUGLUHH20 - 22320 - 223
244GLUGLUJJ20 - 22320 - 223
145ARGARGII20 - 22520 - 225
245ARGARGJJ20 - 22520 - 225

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

-
Components

-
Protein / Sugars , 2 types, 20 molecules ABCDEFGHIJ

#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)
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8WSF8
#3: 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.: 10
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

-
Non-polymers , 5 types, 1883 molecules

#2: Chemical
ChemComp-NCT / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / (S)-(-)-NICOTINE / 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE / Nicotine


Mass: 162.232 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C10H14N2 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1801 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.59 % / Description: block
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.45 M ammonium phosphate monobasic 2 % glycerol 2 % IPA

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54157 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 8, 2016 / Details: Varimax Cu-VHF
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54157 Å / Relative weight: 1
ReflectionResolution: 2.2→25.2 Å / Num. obs: 176070 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 27.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.115 / Net I/σ(I): 8.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 8731 / CC1/2: 0.675 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xys
Resolution: 2.2→25.2 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.302 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23515 8653 4.9 %RANDOM
Rwork0.20286 ---
obs0.20444 167118 99.71 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.896 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å2-0.24 Å2
2--1.53 Å20 Å2
3---0.46 Å2
Refinement stepCycle: 1 / Resolution: 2.2→25.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16502 0 568 1801 18871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217469
X-RAY DIFFRACTIONr_bond_other_d0.0080.0215600
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.97923763
X-RAY DIFFRACTIONr_angle_other_deg0.9723.00136263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2055.0172057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95724.396803
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99152762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2591599
X-RAY DIFFRACTIONr_chiral_restr0.0890.22665
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119006
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023516
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_it5.9023.0398250
X-RAY DIFFRACTIONr_mcbond_other5.9023.0388249
X-RAY DIFFRACTIONr_mcangle_it6.8494.52910295
X-RAY DIFFRACTIONr_mcangle_other6.8494.53110296
X-RAY DIFFRACTIONr_scbond_it9.2733.8469219
X-RAY DIFFRACTIONr_scbond_other9.2723.8469220
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.0365.49613469
X-RAY DIFFRACTIONr_long_range_B_refined12.97638.50719360
X-RAY DIFFRACTIONr_long_range_B_other13.00337.98318945
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)
11A131980.04
12B131980.04
21A133900.04
22C133900.04
31A133200.05
32D133200.05
41A133620.04
42E133620.04
51A133200.04
52F133200.04
61A133360.05
62G133360.05
71A132140.04
72H132140.04
81A133240.05
82I133240.05
91A133160.04
92J133160.04
101B132780.03
102C132780.03
111B132400.04
112D132400.04
121B132780.04
122E132780.04
131B132900.04
132F132900.04
141B132320.04
142G132320.04
151B132320.04
152H132320.04
161B132620.04
162I132620.04
171B132840.04
172J132840.04
181C133920.04
182D133920.04
191C134440.02
192E134440.02
201C134320.03
202F134320.03
211C134340.04
212G134340.04
221C132700.03
222H132700.03
231C134280.03
232I134280.03
241C134140.03
242J134140.03
251D134000.04
252E134000.04
261D133560.05
262F133560.05
271D134880.04
272G134880.04
281D132760.05
282H132760.05
291D134540.04
292I134540.04
301D133560.05
302J133560.05
311E134580.02
312F134580.02
321E133540.04
322G133540.04
331E132660.03
332H132660.03
341E134140.04
342I134140.04
351E134580.02
352J134580.02
361F133500.04
362G133500.04
371F132320.04
372H132320.04
381F134100.04
382I134100.04
391F134840.03
392J134840.03
401G132380.03
402H132380.03
411G134560.03
412I134560.03
421G133420.05
422J133420.05
431H132640.04
432I132640.04
441H132240.04
442J132240.04
451I134400.04
452J134400.04
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 641 -
Rwork0.273 12260 -
obs--99.7 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more