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- PDB-7pd6: Crystal structure of Lymnaea stagnalis Acetylcholine-binding prot... -

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Basic information

Entry
Database: PDB / ID: 7pd6
TitleCrystal structure of Lymnaea stagnalis Acetylcholine-binding protein (Ls-AChBP) Q55R/M114V double mutant complexed with Sulfoxaflor
ComponentsAcetylcholine-binding protein
KeywordsCHOLINE-BINDING PROTEIN / acetylcholine / protein / mutant / SIGNALING PROTEIN
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / synaptic cleft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / 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 / Ig-like domain profile. / Immunoglobulin-like domain
Similarity search - Domain/homology
Sulfoxaflor / Acetylcholine-binding protein
Similarity search - Component
Biological speciesLymnaea stagnalis (great pond snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMontgomery, M.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Structural Biology-Guided Design, Synthesis, and Biological Evaluation of Novel Insect Nicotinic Acetylcholine Receptor Orthosteric Modulators.
Authors: Montgomery, M. / Rendine, S. / Zimmer, C.T. / Elias, J. / Schaetzer, J. / Pitterna, T. / Benfatti, F. / Skaljac, M. / Bigot, A.
History
DepositionAug 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AaA: Acetylcholine-binding protein
BaB: Acetylcholine-binding protein
CaC: Acetylcholine-binding protein
DaD: Acetylcholine-binding protein
EaE: Acetylcholine-binding protein
FaF: Acetylcholine-binding protein
GaG: Acetylcholine-binding protein
HaH: Acetylcholine-binding protein
IaI: Acetylcholine-binding protein
JJJ: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,68019
Polymers238,18410
Non-polymers2,4959
Water6,305350
1
AaA: Acetylcholine-binding protein
BaB: Acetylcholine-binding protein
CaC: Acetylcholine-binding protein
DaD: Acetylcholine-binding protein
EaE: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,47810
Polymers119,0925
Non-polymers1,3865
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13890 Å2
ΔGint-53 kcal/mol
Surface area40500 Å2
MethodPISA
2
FaF: Acetylcholine-binding protein
GaG: Acetylcholine-binding protein
HaH: Acetylcholine-binding protein
IaI: Acetylcholine-binding protein
JJJ: Acetylcholine-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2019
Polymers119,0925
Non-polymers1,1094
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13780 Å2
ΔGint-56 kcal/mol
Surface area40860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.886, 74.367, 130.058
Angle α, β, γ (deg.)90.000, 101.645, 90.000
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA BBB
21Chains AAA CCC
31Chains AAA DDD
41Chains AAA EEE
51Chains AAA FFF
61Chains AAA GGG
71Chains AAA HHH
81Chains AAA III
91Chains AAA JJJ
101Chains BBB CCC
111Chains BBB DDD
121Chains BBB EEE
131Chains BBB FFF
141Chains BBB GGG
151Chains BBB HHH
161Chains BBB III
171Chains BBB JJJ
181Chains CCC DDD
191Chains CCC EEE
201Chains CCC FFF
211Chains CCC GGG
221Chains CCC HHH
231Chains CCC III
241Chains CCC JJJ
251Chains DDD EEE
261Chains DDD FFF
271Chains DDD GGG
281Chains DDD HHH
291Chains DDD III
301Chains DDD JJJ
311Chains EEE FFF
321Chains EEE GGG
331Chains EEE HHH
341Chains EEE III
351Chains EEE JJJ
361Chains FFF GGG
371Chains FFF HHH
381Chains FFF III
391Chains FFF JJJ
401Chains GGG HHH
411Chains GGG III
421Chains GGG JJJ
431Chains HHH III
441Chains HHH JJJ
451Chains III JJJ

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Components

#1: Protein
Acetylcholine-binding protein / ACh-binding protein / AchBP


Mass: 23818.428 Da / Num. of mol.: 10 / Mutation: Q55R, D66N, M114V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymnaea stagnalis (great pond snail) / Production host: Komagataella pastoris (fungus) / References: UniProt: P58154
#2: Chemical
ChemComp-7II / Sulfoxaflor / [methyl-oxidanylidene-[1-[6-(trifluoromethyl)pyridin-3-yl]ethyl]-$l^{6}-sulfanylidene]cyanamide


Mass: 277.266 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H10F3N3OS / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotoxin*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 14-18% PEG3350, 0.1-0.25M diammonium hydrogen citrate, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 1.796→127.381 Å / Num. obs: 117528 / % possible obs: 95 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.9
Reflection shellResolution: 1.796→2.034 Å / Rmerge(I) obs: 1.097 / Num. unique obs: 5876 / CC1/2: 0.613

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
STARANISO2.3.20data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UV6
Resolution: 2→127.381 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.202 / SU B: 12.457 / SU ML: 0.157 / Average fsc free: 0.8975 / Average fsc work: 0.9054 / Cross valid method: FREE R-VALUE / ESU R: 0.288 / ESU R Free: 0.2
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2311 5524 4.866 %
Rwork0.2063 107992 -
all0.208 --
obs-113516 77.418 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.199 Å2
Baniso -1Baniso -2Baniso -3
1--1.233 Å2-0 Å20.254 Å2
2--0.054 Å2-0 Å2
3---0.991 Å2
Refinement stepCycle: LAST / Resolution: 2→127.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15947 0 162 350 16459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01316604
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714961
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.64422714
X-RAY DIFFRACTIONr_angle_other_deg1.3641.57534711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75652013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96121.525938
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.726152713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.47615146
X-RAY DIFFRACTIONr_chiral_restr0.0810.22250
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023585
X-RAY DIFFRACTIONr_nbd_refined0.1940.22400
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.213920
X-RAY DIFFRACTIONr_nbtor_refined0.1650.28060
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.28405
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2498
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0980.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.243
X-RAY DIFFRACTIONr_nbd_other0.2390.2127
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.218
X-RAY DIFFRACTIONr_mcbond_it1.3851.8917992
X-RAY DIFFRACTIONr_mcbond_other1.3851.8917991
X-RAY DIFFRACTIONr_mcangle_it2.2842.8259962
X-RAY DIFFRACTIONr_mcangle_other2.2832.8259963
X-RAY DIFFRACTIONr_scbond_it2.0192.1638612
X-RAY DIFFRACTIONr_scbond_other2.0192.1638613
X-RAY DIFFRACTIONr_scangle_it3.3413.15312731
X-RAY DIFFRACTIONr_scangle_other3.3413.15312732
X-RAY DIFFRACTIONr_lrange_it5.53221.53917368
X-RAY DIFFRACTIONr_lrange_other5.52921.50317343
X-RAY DIFFRACTIONr_ncsr_local_group_10.0960.056014
X-RAY DIFFRACTIONr_ncsr_local_group_20.1010.055990
X-RAY DIFFRACTIONr_ncsr_local_group_30.0890.056000
X-RAY DIFFRACTIONr_ncsr_local_group_40.0830.056063
X-RAY DIFFRACTIONr_ncsr_local_group_50.0710.056258
X-RAY DIFFRACTIONr_ncsr_local_group_60.0990.055969
X-RAY DIFFRACTIONr_ncsr_local_group_70.0940.055988
X-RAY DIFFRACTIONr_ncsr_local_group_80.0860.056045
X-RAY DIFFRACTIONr_ncsr_local_group_90.0850.056012
X-RAY DIFFRACTIONr_ncsr_local_group_100.0930.056236
X-RAY DIFFRACTIONr_ncsr_local_group_110.1020.056043
X-RAY DIFFRACTIONr_ncsr_local_group_120.10.056116
X-RAY DIFFRACTIONr_ncsr_local_group_130.1060.056107
X-RAY DIFFRACTIONr_ncsr_local_group_140.0690.056339
X-RAY DIFFRACTIONr_ncsr_local_group_150.0930.056095
X-RAY DIFFRACTIONr_ncsr_local_group_160.0970.056091
X-RAY DIFFRACTIONr_ncsr_local_group_170.0990.056078
X-RAY DIFFRACTIONr_ncsr_local_group_180.0930.056085
X-RAY DIFFRACTIONr_ncsr_local_group_190.0920.056206
X-RAY DIFFRACTIONr_ncsr_local_group_200.1110.056043
X-RAY DIFFRACTIONr_ncsr_local_group_210.0880.056259
X-RAY DIFFRACTIONr_ncsr_local_group_220.0660.056307
X-RAY DIFFRACTIONr_ncsr_local_group_230.0920.056113
X-RAY DIFFRACTIONr_ncsr_local_group_240.0850.056139
X-RAY DIFFRACTIONr_ncsr_local_group_250.0810.056119
X-RAY DIFFRACTIONr_ncsr_local_group_260.1020.055970
X-RAY DIFFRACTIONr_ncsr_local_group_270.0910.056102
X-RAY DIFFRACTIONr_ncsr_local_group_280.0840.056112
X-RAY DIFFRACTIONr_ncsr_local_group_290.050.056365
X-RAY DIFFRACTIONr_ncsr_local_group_300.0790.056146
X-RAY DIFFRACTIONr_ncsr_local_group_310.0980.056121
X-RAY DIFFRACTIONr_ncsr_local_group_320.0830.056218
X-RAY DIFFRACTIONr_ncsr_local_group_330.080.056251
X-RAY DIFFRACTIONr_ncsr_local_group_340.0870.056154
X-RAY DIFFRACTIONr_ncsr_local_group_350.0650.056258
X-RAY DIFFRACTIONr_ncsr_local_group_360.1060.056007
X-RAY DIFFRACTIONr_ncsr_local_group_370.1050.056029
X-RAY DIFFRACTIONr_ncsr_local_group_380.1010.056029
X-RAY DIFFRACTIONr_ncsr_local_group_390.0960.056064
X-RAY DIFFRACTIONr_ncsr_local_group_400.0820.056167
X-RAY DIFFRACTIONr_ncsr_local_group_410.0940.056112
X-RAY DIFFRACTIONr_ncsr_local_group_420.0870.056085
X-RAY DIFFRACTIONr_ncsr_local_group_430.0920.056171
X-RAY DIFFRACTIONr_ncsr_local_group_440.080.056182
X-RAY DIFFRACTIONr_ncsr_local_group_450.0850.056197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.31580.29229190.293107620.7890.77928.59130.283
2.052-2.1080.272000.28342460.283104990.8320.81642.34690.273
2.108-2.1690.3252700.27949550.282102250.7980.82551.10020.264
2.169-2.2360.2912570.26453890.26599280.840.85456.86950.244
2.236-2.3090.2832870.25657730.25796000.8650.87263.1250.233
2.309-2.390.2713140.25162770.25293420.880.88470.55230.225
2.39-2.4810.283370.25167460.25290060.8590.88478.64760.221
2.481-2.5820.263610.24971050.2586780.8850.88986.03360.223
2.582-2.6970.2863780.24174440.24383170.8780.89494.04830.216
2.697-2.8280.2473880.23374810.23479500.9030.90698.98110.208
2.828-2.9810.2543450.21872310.2275780.910.92399.97360.198
2.981-3.1620.2463490.21667730.21771250.9140.92599.95790.201
3.162-3.380.2273000.20664620.20767700.9280.9499.88180.197
3.38-3.650.2133360.19859480.19962870.9380.94299.95230.197
3.65-3.9990.2252890.18154920.18357840.9410.95599.94810.183
3.999-4.470.1582860.15249710.15252580.970.97299.9810.165
4.47-5.160.1862430.15544220.15646700.9640.97299.89290.173
5.16-6.3180.2252020.17737350.17939470.9570.96699.74660.199
6.318-8.9230.191410.1829320.1830840.9610.96599.64330.209
8.923-127.3810.3830.24716750.24917680.9620.96199.43440.304
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)
12.5467-1.0410.32072.4771-0.07871.46260.02360.25860.0867-0.4412-0.1554-0.430.07740.28640.13180.28720.03110.11920.1230.0710.111430.07617.205722.3648
21.7849-0.8769-0.46283.0522-0.09881.42060.0465-0.08190.17830.266-0.059-0.3757-0.1050.17270.01260.1304-0.0349-0.01270.12320.01390.059132.088411.047648.438
33.4603-0.61750.50652.0713-0.03670.84620.0292-0.1484-0.05390.1621-0.00380.10850.1003-0.0587-0.02530.1347-0.0204-0.00170.08520.02620.014318.1787-11.68952.6133
41.6168-1.1756-0.15912.2207-0.31080.70710.08090.0989-0.136-0.3959-0.03840.22360.1357-0.0775-0.04250.2987-0.021-0.10450.0920.00490.10187.6567-19.001629.3198
51.926-0.4773-0.24732.9955-0.10141.22140.05160.30740.086-0.8093-0.0650.10160.240.11030.01340.58280.0323-0.0540.1740.02340.030615.5687-1.472110.9318
62.52930.9451-0.16342.2142-0.70791.4425-0.0853-0.0130.17050.02810.05360.297-0.148-0.21520.03170.17870.0428-0.02450.0655-0.03870.0732-45.328754.665142.1959
72.07360.5847-0.15382.73140.72551.7385-0.06990.22350.2323-0.4062-0.01870.2149-0.2271-0.19570.08850.31270.0163-0.11450.1860.03370.0658-45.687648.519816.1681
83.10820.45390.97431.6822-0.10051.29650.01520.272-0.2062-0.2369-0.0459-0.16770.05150.14960.03070.24080.003-0.00190.1992-0.01330.034-31.981325.764712.7012
92.13161.0572-0.06981.54140.18071.0333-0.0043-0.0199-0.09430.05840.0211-0.11820.16480.1537-0.01680.19610.0352-0.02490.0814-0.01120.105-22.403718.331936.2929
102.09740.335-0.10132.2259-0.24240.6785-0.0807-0.18740.0140.2015-0.0054-0.125-0.01340.00480.08610.19750.0207-0.03750.0657-0.00510.0193-31.078336.123354.2715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA0 - 204
2X-RAY DIFFRACTION2ALLBBB0 - 204
3X-RAY DIFFRACTION3ALLCCC0 - 204
4X-RAY DIFFRACTION4ALLDDD0 - 207
5X-RAY DIFFRACTION5ALLEEE0 - 204
6X-RAY DIFFRACTION6ALLFFF0 - 204
7X-RAY DIFFRACTION7ALLGGG0 - 204
8X-RAY DIFFRACTION8ALLHHH0 - 204
9X-RAY DIFFRACTION9ALLIII0 - 207
10X-RAY DIFFRACTION10ALLJJJ2 - 204

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