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- PDB-3p50: Structure of propofol bound to a pentameric ligand-gated ion chan... -

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Basic information

Entry
Database: PDB / ID: 3p50
TitleStructure of propofol bound to a pentameric ligand-gated ion channel, GLIC
ComponentsGlr4197 protein
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / Ligand-gated ion channel
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
2,6-BIS(1-METHYLETHYL)PHENOL / DIUNDECYL PHOSPHATIDYL CHOLINE / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsNury, H. / Van Renterghem, C. / Weng, Y. / Tran, A. / Baaden, M. / Dufresne, V. / Changeux, J.P. / Sonner, J.M. / Delarue, M. / Corringer, P.J.
CitationJournal: Nature / Year: 2011
Title: X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel
Authors: Nury, H. / Van Renterghem, C. / Weng, Y. / Tran, A. / Baaden, M. / Dufresne, V. / Changeux, J.P. / Sonner, J.M. / Delarue, M. / Corringer, P.J.
History
DepositionOct 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,92726
Polymers181,7445
Non-polymers10,18321
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21550 Å2
ΔGint-149 kcal/mol
Surface area63360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.130, 132.780, 159.970
Angle α, β, γ (deg.)90.00, 102.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glr4197 protein


Mass: 36348.805 Da / Num. of mol.: 5 / Fragment: residues in UNP 44-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glr4197 / Plasmid: PETB20b / 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.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Chemical
ChemComp-PFL / 2,6-BIS(1-METHYLETHYL)PHENOL / 2,6-DIISOPROPYLPHENOL / PROPOFOL


Mass: 178.271 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H18O
#4: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.170334 Å3/Da / Density % sol: 76.210434 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.3→25 Å / Num. obs: 51485 / % possible obs: 92.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 73.71 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 8.7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.3 / % possible all: 94.2

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Processing

Software
NameVersionClassification
CCP4model building
BUSTER2.9.3refinement
XDSdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EAM

3eam


Resolution: 3.3→12 Å / Cor.coef. Fo:Fc: 0.8635 / Cor.coef. Fo:Fc free: 0.8603 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 2554 5.05 %RANDOM
Rwork0.1832 ---
obs0.1842 50543 90.63 %-
Displacement parametersBiso max: 171.57 Å2 / Biso mean: 69.8064 Å2 / Biso min: 6.97 Å2
Baniso -1Baniso -2Baniso -3
1--13.9172 Å20 Å234.632 Å2
2---0.8237 Å20 Å2
3---14.7409 Å2
Refine analyzeLuzzati coordinate error obs: 0.556 Å
Refinement stepCycle: LAST / Resolution: 3.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12625 0 355 23 13003
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4591SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes275HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1885HARMONIC5
X-RAY DIFFRACTIONt_it13306HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
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_contact14985SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13306HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg18132HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion20.11
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2698 208 5.44 %
Rwork0.2327 3614 -
all0.2347 3822 -
obs--90.63 %

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