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- PDB-3uub: The GLIC pentameric Ligand-Gated Ion Channel Loop2-21' mutant red... -

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Basic information

Entry
Database: PDB / ID: 3uub
TitleThe GLIC pentameric Ligand-Gated Ion Channel Loop2-21' mutant reduced in solution
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / Cys-loop receptor family
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane transporter complex / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / 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 / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / 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
DIUNDECYL PHOSPHATIDYL CHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSauguet, L. / Nury, H. / Corringer, P.J. / Delarue, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: A locally closed conformation of a bacterial pentameric proton-gated ion channel.
Authors: Prevost, M.S. / Sauguet, L. / Nury, H. / Van Renterghem, C. / Huon, C. / Poitevin, F. / Baaden, M. / Delarue, M. / Corringer, P.J.
History
DepositionNov 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Jun 27, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Glr4197 protein
B: Glr4197 protein
C: Glr4197 protein
D: Glr4197 protein
E: Glr4197 protein
F: Glr4197 protein
G: Glr4197 protein
H: Glr4197 protein
I: Glr4197 protein
J: Glr4197 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,46364
Polymers365,25010
Non-polymers25,21354
Water1,982110
1
A: Glr4197 protein
B: Glr4197 protein
C: Glr4197 protein
D: Glr4197 protein
E: Glr4197 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,23132
Polymers182,6255
Non-polymers12,60627
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34340 Å2
ΔGint-172 kcal/mol
Surface area63100 Å2
MethodPISA
2
F: Glr4197 protein
G: Glr4197 protein
H: Glr4197 protein
I: Glr4197 protein
J: Glr4197 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,23132
Polymers182,6255
Non-polymers12,60627
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33830 Å2
ΔGint-167 kcal/mol
Surface area63200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.130, 133.490, 319.690
Angle α, β, γ (deg.)90.00, 102.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 22 molecules ABCDEFGHIJ

#1: Protein
Glr4197 protein / GLIC / ligand-gated ion channel


Mass: 36524.977 Da / Num. of mol.: 10 / Fragment: UNP residues 44-359 / Mutation: C27S,K33C,N245C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 4 types, 152 molecules

#2: Chemical...
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 5.19 Å3/Da / Density % sol: 76.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 15% PEG4000, 0.4 M sodium thiocyanate, 0.1 M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→49.4 Å / Num. all: 165430 / Num. obs: 165264 / % possible obs: 99.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 73.05 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.05 / Net I/σ(I): 11.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 2.3 / Num. unique all: 24023 / Rsym value: 0.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EAM

3eam


Resolution: 2.9→49.36 Å / Cor.coef. Fo:Fc: 0.8589 / Cor.coef. Fo:Fc free: 0.8701 / SU R Cruickshank DPI: 0.412 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.375 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.254
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 8306 5.03 %RANDOM
Rwork0.2178 ---
obs0.218 165245 99.9 %-
Displacement parametersBiso mean: 63.2 Å2
Baniso -1Baniso -2Baniso -3
1--11.6475 Å20 Å224.6758 Å2
2---2.7709 Å20 Å2
3---14.4184 Å2
Refine analyzeLuzzati coordinate error obs: 0.388 Å
Refinement stepCycle: LAST / Resolution: 2.9→49.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25200 0 742 110 26052
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9197SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes510HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3763HARMONIC5
X-RAY DIFFRACTIONt_it26572HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3521SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact29168SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d26572HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg36127HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion17.69
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2564 619 5.08 %
Rwork0.2375 11566 -
all0.2385 12185 -
obs--99.9 %
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)
10.1667-0.06960.15990.14-0.06010.42950.00290.02280.021-0.00710.00210.0192-0.0196-0.0252-0.0050.01590.0333-0.018-0.00420.0013-0.021639.515219.597129.2737
20.5502-0.0070.43040.03230.04130.57010.01220.0256-0.02210.0224-0.02290.0382-0.0163-0.02210.0108-0.02940.0182-0.01040.0247-0.0168-0.010427.8786-1.71235.7284
30.15170.03980.24380.2810.14510.5060.01150.0113-0.0359-0.0195-0.02560.02380.0049-0.00260.01420.00290.0068-0.0309-0.0048-0.0252-0.009142.2809-21.243829.0323
40.1472-0.01080.13990.13930.0640.51880.00230.0357-0.0137-0.0372-0.0081-0.0174-0.00030.00150.00580.00190.0174-0.00860.0028-0.0307-0.00863.0492-11.963718.154
50.15-0.04780.1410.1592-0.21010.54430.0040.03440.0185-0.0358-0.0017-0.0099-0.0162-0.0056-0.00230.0164-0.0013-0.0059-0.00820.0189-0.018161.342613.275718.3032
60.14480.00620.1940.17590.00390.5104-0.00070.01270.0283-0.00810.00720.026-0.0173-0.0123-0.00650.01570.0281-0.017-0.01860.0137-0.01475.587622.746185.9422
70.4426-0.0480.2920.06080.03620.36680.00430.0284-0.00170.0211-0.00540.0334-0.0064-0.02430.0011-0.03060.0171-0.00780.0158-0.0048-0.0039-6.80761.5803191.5548
80.19930.06940.19280.18830.10440.48310.00440.0325-0.0295-0.0175-0.01280.01120.0126-0.01750.00840.00180.0169-0.0255-0.0127-0.027-0.00046.8952-18.2224184.2257
90.0848-0.02540.17090.20690.09770.6955-0.00150.0084-0.0035-0.0581-0.0021-0.01820.00230.0090.00370.00770.0169-0.0138-0.0065-0.0231-0.009327.9093-9.2348173.5217
100.0742-0.02560.10440.2953-0.25550.5077-0.0047-0.0030.0199-0.0460.0108-0.0026-0.00580.0136-0.0060.02-0.014-0.0098-0.01350.022-0.018927.137116.0209174.6552
110.63110.01670.0720.63540.04350.68860.00060.0079-0.0008-0.0037-0.00150.0032-0.0017-0.00470.00090.0033-0.00050.00370.0009-0.00020.006557.9098-0.28246.2822
120.7148-0.06060.22860.55540.0630.93140.00050.0072-0.0016-0.0039-0.00020.00320.0009-0.0041-0.00020.00340.00020.00220.0028-0.00020.006523.11011.4695202.1749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A5 - 315
2X-RAY DIFFRACTION2{ B|* }B5 - 315
3X-RAY DIFFRACTION3{ C|* }C5 - 315
4X-RAY DIFFRACTION4{ D|* }D5 - 315
5X-RAY DIFFRACTION5{ E|* }E5 - 315
6X-RAY DIFFRACTION6{ F|* }F5 - 315
7X-RAY DIFFRACTION7{ G|* }G5 - 315
8X-RAY DIFFRACTION8{ H|* }H5 - 315
9X-RAY DIFFRACTION9{ I|* }I5 - 315
10X-RAY DIFFRACTION10{ J|* }J5 - 315
11X-RAY DIFFRACTION11A318 - 321
12X-RAY DIFFRACTION11B318 - 320
13X-RAY DIFFRACTION11C318 - 319
14X-RAY DIFFRACTION11D318 - 320
15X-RAY DIFFRACTION11E318 - 320
16X-RAY DIFFRACTION12F318 - 320
17X-RAY DIFFRACTION12G318 - 319
18X-RAY DIFFRACTION12H318 - 321
19X-RAY DIFFRACTION12I318 - 320
20X-RAY DIFFRACTION12J318 - 320

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