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- PDB-5hcm: The GLIC pentameric Ligand-Gated Ion Channel 2-21' cross-linked m... -

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Basic information

Entry
Database: PDB / ID: 5hcm
TitleThe GLIC pentameric Ligand-Gated Ion Channel 2-21' cross-linked mutant complexed to bromoform
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / ion channel / receptor / anaesthetic
Function / homology
Function and homology information


sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium 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 / 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
TRIBROMOMETHANE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.15 Å
AuthorsShahsavar, A. / Sauguet, L. / Delarue, M.
CitationJournal: Structure / Year: 2016
Title: Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel.
Authors: Laurent, B. / Murail, S. / Shahsavar, A. / Sauguet, L. / Delarue, M. / Baaden, M.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proton-gated ion channel
B: Proton-gated ion channel
C: Proton-gated ion channel
D: Proton-gated ion channel
E: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,9577
Polymers181,1935
Non-polymers7632
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23230 Å2
ΔGint-138 kcal/mol
Surface area64100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.268, 130.934, 155.760
Angle α, β, γ (deg.)90.00, 100.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC


Mass: 36238.688 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: C27S, K33C, N245C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8
#2: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Chemical ChemComp-MBR / TRIBROMOMETHANE / Bromoform


Mass: 252.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHBr3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.91 Å3/Da / Density % sol: 74.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG 4000 12-15%, 0.1 M Na Acetate pH4, 0.4M NaSCN, 15% glycerol
PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.15→48 Å / Num. obs: 60505 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 78.02 Å2 / Net I/σ(I): 13

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
RefinementResolution: 3.15→31.75 Å / Cor.coef. Fo:Fc: 0.8766 / Cor.coef. Fo:Fc free: 0.8703 / SU R Cruickshank DPI: 0.815 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.679 / SU Rfree Blow DPI: 0.328 / SU Rfree Cruickshank DPI: 0.345
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 3062 5.07 %RANDOM
Rwork0.2303 ---
obs0.2308 60453 99.75 %-
Displacement parametersBiso mean: 82.63 Å2
Baniso -1Baniso -2Baniso -3
1--23.0261 Å20 Å224.8526 Å2
2--15.9126 Å20 Å2
3---7.1135 Å2
Refine analyzeLuzzati coordinate error obs: 0.698 Å
Refinement stepCycle: 1 / Resolution: 3.15→31.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12600 0 16 0 12616
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812954HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0717708HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4284SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes255HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1870HARMONIC5
X-RAY DIFFRACTIONt_it12954HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.81
X-RAY DIFFRACTIONt_other_torsion18.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1760SEMIHARMONIC5
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_contact14364SEMIHARMONIC4
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2912 243 5.49 %
Rwork0.2842 4183 -
all0.2846 4426 -
obs--99.75 %
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)
11.6207-0.11931.5430.6438-0.08152.69160.0709-0.09610.1062-0.1357-0.05020.0784-0.0263-0.1237-0.02070.22440.0361-0.1715-0.2617-0.0112-0.2187.5385-3.9655183.4261
21.40320.12741.72250.48840.31432.68460.0218-0.07940.01740.0719-0.05070.13410.0128-0.11750.02890.09920.0062-0.118-0.11740.011-0.1716177.4677-26.3911188.8584
30.95830.20951.02860.74710.45132.43460.0202-0.0053-0.0806-0.1488-0.02960.10870.04290.03790.00940.20160.0282-0.1935-0.2416-0.0015-0.1522192.7306-44.4596180.6424
40.8185-0.04130.95260.99950.07792.9936-0.00760.0727-0.0709-0.3145-0.05-0.0328-0.10.15710.05760.13520.0245-0.1437-0.2207-0.0355-0.1708212.6785-32.9746169.519
50.7037-0.27350.92390.741-0.60562.759-0.0306-0.01670.0834-0.15550.0189-0.0668-0.08480.01110.01170.2588-0.0414-0.1568-0.23830.0138-0.1922209.3515-8.1195171.4426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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