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- PDB-2yoe: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 2yoe
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with GABA and flurazepam
ComponentsCYS-LOOP LIGAND-GATED ION CHANNEL
KeywordsTRANSPORT PROTEIN / CYS-LOOP RECEPTOR / GABA-A RECEPTOR / BENZODIAZEPINE
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / plasma 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-AMINO-BUTANOIC ACID / Flurazepam / Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesERWINIA CHRYSANTHEMI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsSpurny, R. / Brams, M. / Nury, H. / Legrand, P. / Ulens, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Pentameric Ligand-Gated Ion Channel Elic is Activated by Gaba and Modulated by Benzodiazepines.
Authors: Spurny, R. / Ramerstorfer, J. / Price, K. / Brams, M. / Ernst, M. / Nury, H. / Verheij, M. / Legrand, P. / Bertrand, D. / Bertrand, S. / Dougherty, D.A. / De Esch, I.J.P. / Corringer, P. / ...Authors: Spurny, R. / Ramerstorfer, J. / Price, K. / Brams, M. / Ernst, M. / Nury, H. / Verheij, M. / Legrand, P. / Bertrand, D. / Bertrand, S. / Dougherty, D.A. / De Esch, I.J.P. / Corringer, P. / Sieghart, W. / Lummis, S.C.R. / Ulens, C.
History
DepositionOct 23, 2012Deposition site: PDBE / Processing site: PDBE
SupersessionOct 31, 2012ID: 4A96
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYS-LOOP LIGAND-GATED ION CHANNEL
B: CYS-LOOP LIGAND-GATED ION CHANNEL
C: CYS-LOOP LIGAND-GATED ION CHANNEL
D: CYS-LOOP LIGAND-GATED ION CHANNEL
E: CYS-LOOP LIGAND-GATED ION CHANNEL
F: CYS-LOOP LIGAND-GATED ION CHANNEL
G: CYS-LOOP LIGAND-GATED ION CHANNEL
H: CYS-LOOP LIGAND-GATED ION CHANNEL
I: CYS-LOOP LIGAND-GATED ION CHANNEL
J: CYS-LOOP LIGAND-GATED ION CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,42813
Polymers353,83410
Non-polymers5943
Water0
1
F: CYS-LOOP LIGAND-GATED ION CHANNEL
G: CYS-LOOP LIGAND-GATED ION CHANNEL
H: CYS-LOOP LIGAND-GATED ION CHANNEL
I: CYS-LOOP LIGAND-GATED ION CHANNEL
J: CYS-LOOP LIGAND-GATED ION CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,0206
Polymers176,9175
Non-polymers1031
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25490 Å2
ΔGint-147.8 kcal/mol
Surface area65190 Å2
MethodPISA
2
A: CYS-LOOP LIGAND-GATED ION CHANNEL
B: CYS-LOOP LIGAND-GATED ION CHANNEL
C: CYS-LOOP LIGAND-GATED ION CHANNEL
D: CYS-LOOP LIGAND-GATED ION CHANNEL
E: CYS-LOOP LIGAND-GATED ION CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,4087
Polymers176,9175
Non-polymers4912
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25480 Å2
ΔGint-145.4 kcal/mol
Surface area65090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.771, 266.512, 110.982
Angle α, β, γ (deg.)90.00, 108.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 11:148 OR RESSEQ 150:317 )
211CHAIN B AND (RESSEQ 11:148 OR RESSEQ 150:317 )
311CHAIN C AND (RESSEQ 11:148 OR RESSEQ 150:317 )
411CHAIN D AND (RESSEQ 11:148 OR RESSEQ 150:317 )
511CHAIN E AND (RESSEQ 11:148 OR RESSEQ 150:317 )
611CHAIN F AND (RESSEQ 11:148 OR RESSEQ 150:317 )
711CHAIN G AND (RESSEQ 11:148 OR RESSEQ 150:317 )
811CHAIN H AND (RESSEQ 11:148 OR RESSEQ 150:317 )
911CHAIN I AND (RESSEQ 11:148 OR RESSEQ 150:317 )
1011CHAIN J AND (RESSEQ 11:148 OR RESSEQ 150:317 )

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Components

#1: Protein
CYS-LOOP LIGAND-GATED ION CHANNEL / ELIC


Mass: 35383.367 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C7B7
#2: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM
#3: Chemical ChemComp-FL7 / Flurazepam / Flurazepam


Mass: 387.878 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClFN3O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.61 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3.8→24.98 Å / Num. obs: 54291 / % possible obs: 95.7 % / Observed criterion σ(I): 2.1 / Redundancy: 3.8 % / Biso Wilson estimate: 115.82 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL0

2vl0


Resolution: 3.9→25.028 Å / SU ML: 0.46 / σ(F): 1.37 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 2561 5.1 %
Rwork0.1852 --
obs0.1875 50420 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 97.77 Å2 / ksol: 0.259 e/Å3
Refinement stepCycle: LAST / Resolution: 3.9→25.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24980 0 41 0 25021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00525700
X-RAY DIFFRACTIONf_angle_d1.09935030
X-RAY DIFFRACTIONf_dihedral_angle_d16.4989210
X-RAY DIFFRACTIONf_chiral_restr0.0813890
X-RAY DIFFRACTIONf_plane_restr0.0054470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2494X-RAY DIFFRACTIONPOSITIONAL
12B2494X-RAY DIFFRACTIONPOSITIONAL0.085
13C2494X-RAY DIFFRACTIONPOSITIONAL0.079
14D2494X-RAY DIFFRACTIONPOSITIONAL0.087
15E2494X-RAY DIFFRACTIONPOSITIONAL0.077
16F2494X-RAY DIFFRACTIONPOSITIONAL0.075
17G2494X-RAY DIFFRACTIONPOSITIONAL0.084
18H2494X-RAY DIFFRACTIONPOSITIONAL0.078
19I2491X-RAY DIFFRACTIONPOSITIONAL0.086
110J2494X-RAY DIFFRACTIONPOSITIONAL0.078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.97480.31921290.30742588X-RAY DIFFRACTION94
3.9748-4.05560.29011520.25732690X-RAY DIFFRACTION97
4.0556-4.14340.28481410.22282692X-RAY DIFFRACTION98
4.1434-4.23930.26031410.20292673X-RAY DIFFRACTION97
4.2393-4.34480.23921280.18642695X-RAY DIFFRACTION97
4.3448-4.46160.21891410.17242697X-RAY DIFFRACTION97
4.4616-4.59210.20861420.15692689X-RAY DIFFRACTION97
4.5921-4.73940.18991690.14952661X-RAY DIFFRACTION97
4.7394-4.90750.22631390.15072667X-RAY DIFFRACTION97
4.9075-5.10250.22431330.15562701X-RAY DIFFRACTION96
5.1025-5.33250.21441460.14342660X-RAY DIFFRACTION96
5.3325-5.61070.20181270.1572677X-RAY DIFFRACTION96
5.6107-5.95780.23521440.16372643X-RAY DIFFRACTION96
5.9578-6.41060.21781450.1782655X-RAY DIFFRACTION95
6.4106-7.04270.27951450.19782659X-RAY DIFFRACTION95
7.0427-8.03220.22671450.18732616X-RAY DIFFRACTION95
8.0322-10.01080.16911360.16052619X-RAY DIFFRACTION94
10.0108-25.02890.25181580.22812577X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4061-0.4390.17941.76542.09467.93670.1287-0.1113-0.18040.24470.05510.5310.0789-0.7975-0.04910.8959-0.18930.1140.880.07350.8767-124.0116-50.9626-44.6775
21.435-0.3669-1.24432.38511.44757.41280.0361-0.1749-0.16690.11620.2051-0.05810.05130.0366-0.11221.00770.10510.07320.50240.03540.8923-103.5019-62.7383-40.2131
31.4327-0.2265-1.16121.33970.61587.22840.1278-0.17910.01870.19460.2417-0.51290.21490.4987-0.35580.85150.07680.07070.5334-0.07020.9308-85.2874-47.2359-42.1466
41.1031-0.2014-1.11210.88811.24348.3350.2406-0.07480.25560.02140.0684-0.4209-0.03090.1496-0.36761.09760.01070.26730.4755-0.04450.9929-94.3818-25.6686-47.6473
50.64970.21470.2351.7110.22594.91420.0385-0.07360.2047-0.15820.16090.2225-1.0267-0.3794-0.15740.96980.35730.20840.96790.1490.8393-118.4514-27.9832-49.2413
67.1772.1907-0.86011.7917-0.11720.79420.062-1.0320.02990.5224-0.1791-0.12510.0461-0.02030.13910.9580.15060.10590.92440.13761.0231-80.9519-119.1199-17.4647
77.14322.10981.32841.48730.47961.4798-0.3862-0.0212-0.3522-0.16380.1711-0.2190.30670.28350.19830.88190.09180.26830.56180.06561.0836-77.1644-129.786-38.7255
88.35021.01862.43741.43460.28061.2843-0.20920.8405-0.267-0.41690.1301-0.38360.09850.37990.2490.9901-0.1080.31650.6290.02491.0447-79.8-113.2924-56.0416
98.02570.71540.49411.6413-0.29240.8682-0.2675-0.0081-0.2421-0.14190.1146-0.2955-0.15290.11760.33220.94850.04460.05810.5999-0.03391.2237-85.1292-92.3578-45.6113
107.95540.675-0.63271.1265-0.22220.5117-0.2089-0.94890.41050.35030.0637-0.0062-0.19290.11040.21820.90780.10580.06550.8882-0.30630.9884-85.8792-95.9667-21.6705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J

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