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- PDB-3rqu: Crystal structure of a prokaryotic pentameric ligand-gated ion ch... -

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Basic information

Entry
Database: PDB / ID: 3rqu
TitleCrystal structure of 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 / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / 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
Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.089 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)372,09138
Polymers368,79010
Non-polymers3,30128
Water88349
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)186,28121
Polymers184,3955
Non-polymers1,88616
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29590 Å2
ΔGint-133 kcal/mol
Surface area64280 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)185,81017
Polymers184,3955
Non-polymers1,41512
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28450 Å2
ΔGint-139 kcal/mol
Surface area64440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.289, 266.970, 111.074
Angle α, β, γ (deg.)90.00, 107.53, 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

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

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 69.53 %
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: 3.087→29.8 Å / Num. obs: 104053 / % possible obs: 97.4 % / Observed criterion σ(I): 2.2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15

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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: 3.089→24.99 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 28.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 4868 5 %RANDOM
Rwork0.2091 ---
obs0.2106 97441 91.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.463 Å2 / ksol: 0.272 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.8591 Å2-0 Å216.2266 Å2
2---21.1015 Å2-0 Å2
3---4.2423 Å2
Refinement stepCycle: LAST / Resolution: 3.089→24.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25050 0 209 49 25308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625918
X-RAY DIFFRACTIONf_angle_d0.97135286
X-RAY DIFFRACTIONf_dihedral_angle_d15.8379375
X-RAY DIFFRACTIONf_chiral_restr0.0683900
X-RAY DIFFRACTIONf_plane_restr0.0044470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2484X-RAY DIFFRACTIONPOSITIONAL
12B2484X-RAY DIFFRACTIONPOSITIONAL0.037
21A2484X-RAY DIFFRACTIONPOSITIONAL
22C2484X-RAY DIFFRACTIONPOSITIONAL0.031
31A2484X-RAY DIFFRACTIONPOSITIONAL
32D2484X-RAY DIFFRACTIONPOSITIONAL0.038
41A2484X-RAY DIFFRACTIONPOSITIONAL
42E2484X-RAY DIFFRACTIONPOSITIONAL0.031
51A2484X-RAY DIFFRACTIONPOSITIONAL
52F2484X-RAY DIFFRACTIONPOSITIONAL0.031
61A2484X-RAY DIFFRACTIONPOSITIONAL
62G2484X-RAY DIFFRACTIONPOSITIONAL0.034
71A2484X-RAY DIFFRACTIONPOSITIONAL
72H2484X-RAY DIFFRACTIONPOSITIONAL0.035
81A2484X-RAY DIFFRACTIONPOSITIONAL
82I2484X-RAY DIFFRACTIONPOSITIONAL0.04
91A2484X-RAY DIFFRACTIONPOSITIONAL
92J2484X-RAY DIFFRACTIONPOSITIONAL0.03
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0888-3.1990.37093950.34937154X-RAY DIFFRACTION71
3.199-3.32680.41794300.33428457X-RAY DIFFRACTION84
3.3268-3.47780.3394250.28078617X-RAY DIFFRACTION85
3.4778-3.66070.32894960.2599246X-RAY DIFFRACTION92
3.6607-3.88920.25835240.23959618X-RAY DIFFRACTION95
3.8892-4.18820.27734870.22899767X-RAY DIFFRACTION97
4.1882-4.60730.22235260.18499730X-RAY DIFFRACTION96
4.6073-5.26860.19225570.164510010X-RAY DIFFRACTION99
5.2686-6.61740.21835230.17819960X-RAY DIFFRACTION99
6.6174-24.99040.19865050.195410014X-RAY DIFFRACTION98

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