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- PDB-3rqw: Crystal structure of acetylcholine bound to a prokaryotic pentame... -

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Basic information

Entry
Database: PDB / ID: 3rqw
TitleCrystal structure of acetylcholine bound to a prokaryotic pentameric ligand-gated ion channel, ELIC
ComponentsELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
KeywordsTRANSPORT PROTEIN / ion channel / membrane
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
ACETYLCHOLINE / Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.913 Å
AuthorsPan, J.J. / Chen, Q. / Yoshida, K. / Cohen, A. / Kong, X.P. / Xu, Y. / Tang, P.
CitationJournal: Nat Commun / Year: 2012
Title: Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine.
Authors: Pan, J. / Chen, Q. / Willenbring, D. / Yoshida, K. / Tillman, T. / Kashlan, O.B. / Cohen, A. / Kong, X.P. / Xu, Y. / Tang, P.
History
DepositionApr 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references / Other / Structure summary
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
B: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
C: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
D: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
E: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
F: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
G: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
H: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
I: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
J: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,49656
Polymers368,79010
Non-polymers5,70646
Water1,62190
1
A: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
B: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
C: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
D: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
E: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,11526
Polymers184,3955
Non-polymers2,72021
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33050 Å2
ΔGint-108 kcal/mol
Surface area62280 Å2
MethodPISA
2
F: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
G: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
H: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
I: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
J: ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,38030
Polymers184,3955
Non-polymers2,98525
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34260 Å2
ΔGint-113 kcal/mol
Surface area61850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.763, 266.068, 111.162
Angle α, β, γ (deg.)90.00, 107.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29
110
210
111
211
112
212
113
213
114
214
115
215
116
216
117
217
118
218

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and not (resseq 169 or resseq 163)
211chain B
112chain A and not (resseq 169 or resseq 163)
212chain C
113chain A and not (resseq 169 or resseq 163)
213chain D
114chain A and not (resseq 169 or resseq 163)
214chain E
115chain A and not (resseq 169 or resseq 163)
215chain F
116chain A and not (resseq 169 or resseq 163)
216chain G
117chain A and not (resseq 169 or resseq 163)
217chain H
118chain A and not (resseq 169 or resseq 163)
218chain I
119chain A and not (resseq 169 or resseq 163)
219chain J
1110chain C and resseq 323
2110chain D and resseq 323
1111chain C and resseq 323
2111chain E and resseq 323
1112chain C and resseq 323
2112chain A and resseq 323
1113chain C and resseq 323
2113chain B and resseq 323
1114chain C and resseq 323
2114chain H and resseq 323
1115chain C and resseq 323
2115chain I and resseq 323
1116chain C and resseq 323
2116chain J and resseq 323
1117chain C and resseq 323
2117chain F and resseq 323
1118chain C and resseq 323
2118chain G and resseq 323

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

#1: Protein
ELIC Pentameric Ligand Gated Ion Channel from Erwinia Chrysanthemi


Mass: 36879.000 Da / Num. of mol.: 10 / Fragment: UNP residues 22-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (bacteria) / Strain: 3937 / Gene: Dda3937_00520 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4
#2: Chemical
ChemComp-ACH / ACETYLCHOLINE


Mass: 146.207 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C7H16NO2
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 4.04 Å3/Da / Density % sol: 69.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 12% PEG4000, 0.1 M MES, 0.2 M ammonium sulfate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.91→29.8 Å / Num. obs: 124625 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 22.1

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Processing

Software
NameVersionClassification
SSRLBlueIcedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL0

2vl0


Resolution: 2.913→24.977 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 5901 5.02 %RANDOM
Rwork0.2057 ---
obs0.207 117512 92.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.962 Å2 / ksol: 0.279 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-12.7189 Å2-0 Å213.7734 Å2
2---17.8786 Å2-0 Å2
3---5.1597 Å2
Refinement stepCycle: LAST / Resolution: 2.913→24.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25050 0 368 90 25508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826061
X-RAY DIFFRACTIONf_angle_d1.14435466
X-RAY DIFFRACTIONf_dihedral_angle_d16.3549486
X-RAY DIFFRACTIONf_chiral_restr0.0733900
X-RAY DIFFRACTIONf_plane_restr0.0084470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2484X-RAY DIFFRACTIONPOSITIONAL
12B2484X-RAY DIFFRACTIONPOSITIONAL0.043
21A2484X-RAY DIFFRACTIONPOSITIONAL
22C2484X-RAY DIFFRACTIONPOSITIONAL0.04
31A2484X-RAY DIFFRACTIONPOSITIONAL
32D2484X-RAY DIFFRACTIONPOSITIONAL0.046
41A2484X-RAY DIFFRACTIONPOSITIONAL
42E2484X-RAY DIFFRACTIONPOSITIONAL0.04
51A2484X-RAY DIFFRACTIONPOSITIONAL
52F2484X-RAY DIFFRACTIONPOSITIONAL0.037
61A2484X-RAY DIFFRACTIONPOSITIONAL
62G2484X-RAY DIFFRACTIONPOSITIONAL0.048
71A2484X-RAY DIFFRACTIONPOSITIONAL
72H2484X-RAY DIFFRACTIONPOSITIONAL0.044
81A2484X-RAY DIFFRACTIONPOSITIONAL
82I2484X-RAY DIFFRACTIONPOSITIONAL0.045
91A2484X-RAY DIFFRACTIONPOSITIONAL
92J2484X-RAY DIFFRACTIONPOSITIONAL0.037
101C10X-RAY DIFFRACTIONPOSITIONAL
102D10X-RAY DIFFRACTIONPOSITIONAL0.044
111C10X-RAY DIFFRACTIONPOSITIONAL
112E10X-RAY DIFFRACTIONPOSITIONAL0.024
121C10X-RAY DIFFRACTIONPOSITIONAL
122A10X-RAY DIFFRACTIONPOSITIONAL0.034
131C10X-RAY DIFFRACTIONPOSITIONAL
132B10X-RAY DIFFRACTIONPOSITIONAL0.038
141C10X-RAY DIFFRACTIONPOSITIONAL
142H10X-RAY DIFFRACTIONPOSITIONAL0.026
151C10X-RAY DIFFRACTIONPOSITIONAL
152I10X-RAY DIFFRACTIONPOSITIONAL0.069
161C10X-RAY DIFFRACTIONPOSITIONAL
162J10X-RAY DIFFRACTIONPOSITIONAL0.035
171C10X-RAY DIFFRACTIONPOSITIONAL
172F10X-RAY DIFFRACTIONPOSITIONAL0.029
181C10X-RAY DIFFRACTIONPOSITIONAL
182G10X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.913-3.0170.36264920.33559067X-RAY DIFFRACTION75
3.017-3.13750.31485490.290110376X-RAY DIFFRACTION86
3.1375-3.280.31165690.263710767X-RAY DIFFRACTION89
3.28-3.45260.28415840.241910891X-RAY DIFFRACTION91
3.4526-3.66820.25685940.214611450X-RAY DIFFRACTION95
3.6682-3.95050.22275940.201111706X-RAY DIFFRACTION97
3.9505-4.34610.23086220.197411787X-RAY DIFFRACTION98
4.3461-4.97070.19216740.163911702X-RAY DIFFRACTION97
4.9707-6.24630.20086320.180411965X-RAY DIFFRACTION99
6.2463-24.97780.22455910.211111900X-RAY DIFFRACTION98

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