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- PDB-3uq7: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 3uq7
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) mutant L240S F247L (L9S F16L) in presence of 10 mM cysteamine
ComponentsGamma-aminobutyric-acid receptor subunit beta-1
KeywordsTRANSPORT PROTEIN / membrane protein / liganded-gated ion channel
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
Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesErwinia chrysanthemi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsGonzalez-Gutierrez, G. / Lukk, T. / Agarwal, V. / Papke, D. / Nair, S.K. / Grosman, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Mutations that stabilize the open state of the Erwinia chrisanthemi ligand-gated ion channel fail to change the conformation of the pore domain in crystals.
Authors: Gonzalez-Gutierrez, G. / Lukk, T. / Agarwal, V. / Papke, D. / Nair, S.K. / Grosman, C.
History
DepositionNov 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1


Theoretical massNumber of molelcules
Total (without water)369,63010
Polymers369,63010
Non-polymers00
Water00
1
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1


Theoretical massNumber of molelcules
Total (without water)184,8155
Polymers184,8155
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25310 Å2
ΔGint-146 kcal/mol
Surface area65480 Å2
MethodPISA
2
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1


Theoretical massNumber of molelcules
Total (without water)184,8155
Polymers184,8155
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25300 Å2
ΔGint-146 kcal/mol
Surface area65190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.380, 266.450, 110.910
Angle α, β, γ (deg.)90.00, 109.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
31G
41I
51J
61B
71C
81D
91E
101H

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTYRTYRchain 'A' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )AA11 - 14813 - 150
12ASPASPGLNGLNchain 'A' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )AA153 - 287155 - 289
13GLYGLYALAALAchain 'A' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )AA290 - 310292 - 312
21PROPROTYRTYRchain 'F' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )FF11 - 14813 - 150
22ASPASPGLNGLNchain 'F' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )FF153 - 287155 - 289
23GLYGLYALAALAchain 'F' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )FF290 - 310292 - 312
31PROPROTYRTYRchain 'G' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )GG11 - 14813 - 150
32ASPASPGLNGLNchain 'G' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )GG153 - 287155 - 289
33GLYGLYALAALAchain 'G' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )GG290 - 310292 - 312
41PROPROTYRTYRchain 'I' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )II11 - 14813 - 150
42ASPASPGLNGLNchain 'I' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )II153 - 287155 - 289
43GLYGLYALAALAchain 'I' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )II290 - 310292 - 312
51PROPROTYRTYRchain 'J' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )JJ11 - 14813 - 150
52ASPASPGLNGLNchain 'J' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )JJ153 - 287155 - 289
53GLYGLYALAALAchain 'J' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )JJ290 - 310292 - 312
61PROPROTYRTYRchain 'B' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )BB11 - 14813 - 150
62ASPASPGLNGLNchain 'B' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )BB153 - 287155 - 289
63GLYGLYALAALAchain 'B' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )BB290 - 310292 - 312
71PROPROTYRTYRchain 'C' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )CC11 - 14813 - 150
72ASPASPGLNGLNchain 'C' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )CC153 - 287155 - 289
73GLYGLYALAALAchain 'C' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )CC290 - 310292 - 312
81PROPROTYRTYRchain 'D' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )DD11 - 14813 - 150
82ASPASPGLNGLNchain 'D' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )DD153 - 287155 - 289
83GLYGLYALAALAchain 'D' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )DD290 - 310292 - 312
91PROPROTYRTYRchain 'E' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )EE11 - 14813 - 150
92ASPASPGLNGLNchain 'E' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )EE153 - 287155 - 289
93GLYGLYALAALAchain 'E' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )EE290 - 310292 - 312
101PROPROTYRTYRchain 'H' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )HH11 - 14813 - 150
102ASPASPGLNGLNchain 'H' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )HH153 - 287155 - 289
103GLYGLYALAALAchain 'H' and (resseq 11:148 or resseq 153:287 or resseq 290:310 )HH290 - 310292 - 312

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Components

#1: Protein
Gamma-aminobutyric-acid receptor subunit beta-1 / ELIC


Mass: 36963.035 Da / Num. of mol.: 10 / Mutation: L239S,F246L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erwinia chrysanthemi (bacteria) / Strain: 3937 / Gene: Dda3937_00520 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4

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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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10-12% PEG4000, 200 mM ammonium sulfate, 50 mM N-(2-acetamido)iminodiacetic acid (ADA), pH 6.5-6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 18, 2011
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.8→133.225 Å / Num. obs: 56196 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 88.153 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.8-3.90.6912.9426921418999.5
3.9-4.010.5653.5426026403899.9
4.01-4.120.4654.1725619396599.7
4.12-4.250.3585.3524938385399.7
4.25-4.390.2896.52241503731100
4.39-4.540.2178.4223146357899.8
4.54-4.710.1919.4922474348099.9
4.71-4.910.17510.2421776336999.9
4.91-5.120.16510.820683320199.8
5.12-5.370.16210.8919892307799.9
5.37-5.660.16311.1918991294399.7
5.66-6.010.15111.9817803276299.9
6.01-6.420.14812.1916830260799.9
6.42-6.940.1313.715688244299.9
6.94-7.60.09318.4114188221699.6
7.6-8.50.05925.5112896203299.8
8.5-9.810.03835.2211231177799.7
9.81-12.020.0341.249421151499.5
12.02-16.990.0343.256882117199.7
16.990.02845.56137025137.7

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Processing

Software
NameVersionClassificationNB
PHENIXdev_897refinement
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL0

2vl0


Resolution: 3.8→19.966 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.4 / σ(F): 1.99 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 2809 5 %
Rwork0.2149 --
obs0.2164 56162 99.87 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.078 Å2 / ksol: 0.263 e/Å3
Displacement parametersBiso max: 285.96 Å2 / Biso mean: 127.7107 Å2 / Biso min: 44.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.4013 Å2-0 Å21.6037 Å2
2---4.481 Å2-0 Å2
3---3.0797 Å2
Refinement stepCycle: LAST / Resolution: 3.8→19.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25000 0 0 0 25000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01325669
X-RAY DIFFRACTIONf_angle_d1.5734987
X-RAY DIFFRACTIONf_chiral_restr0.1183900
X-RAY DIFFRACTIONf_plane_restr0.0074459
X-RAY DIFFRACTIONf_dihedral_angle_d19.2539219
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2407X-RAY DIFFRACTIONPOSITIONAL0.066
12F2407X-RAY DIFFRACTIONPOSITIONAL0.066
13G2407X-RAY DIFFRACTIONPOSITIONAL0.06
14I2407X-RAY DIFFRACTIONPOSITIONAL0.061
15J2407X-RAY DIFFRACTIONPOSITIONAL0.062
16B2407X-RAY DIFFRACTIONPOSITIONAL0.056
17C2407X-RAY DIFFRACTIONPOSITIONAL0.08
18D2407X-RAY DIFFRACTIONPOSITIONAL0.061
19E2407X-RAY DIFFRACTIONPOSITIONAL0.063
110H2407X-RAY DIFFRACTIONPOSITIONAL0.072
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8-3.86510.36251390.357426492788100
3.8651-3.93490.33711390.33972642278199
3.9349-4.00990.33871410.311126672808100
4.0099-4.09110.30361400.293326722812100
4.0911-4.17930.33081400.2826502790100
4.1793-4.27560.31121400.258626592799100
4.2756-4.38140.25741410.228826852826100
4.3814-4.49860.22811400.209426472787100
4.4986-4.62930.23511410.194126892830100
4.6293-4.77680.2211400.186826642804100
4.7768-4.9450.24531400.193826492789100
4.945-5.13980.21271400.186826622802100
5.1398-5.36940.23461400.185426692809100
5.3694-5.64640.24311410.202126782819100
5.6464-5.99120.23031410.193426732814100
5.9912-6.43930.25921400.204626632803100
6.4393-7.06120.26241420.212526982840100
7.0612-8.02430.1921410.171226722813100
8.0243-9.90020.17481410.150226812822100
9.9002-19.96670.22621420.2212684282699

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