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- PDB-4f8h: X-ray Structure of the Anesthetic Ketamine Bound to the GLIC Pent... -

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Basic information

Entry
Database: PDB / ID: 4f8h
TitleX-ray Structure of the Anesthetic Ketamine Bound to the GLIC Pentameric Ligand-gated Ion Channel
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / ketamine / pentameric ligand-gated ion channel / ion channel / anesthetics
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
Chem-LMD / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (R)-ketamine / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsPan, J.J. / Chen, Q. / Willenbring, D. / Kong, X.P. / Cohen, A. / Xu, Y. / Tang, P.
CitationJournal: Structure / Year: 2012
Title: Structure of the Pentameric Ligand-Gated Ion Channel GLIC Bound with Anesthetic Ketamine.
Authors: Pan, J. / Chen, Q. / Willenbring, D. / Mowrey, D. / Kong, X.P. / Cohen, A. / Divito, C.B. / Xu, Y. / Tang, P.
History
DepositionMay 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Jun 13, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 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)193,71126
Polymers181,3895
Non-polymers12,32221
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33650 Å2
ΔGint-219 kcal/mol
Surface area60940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.069, 132.742, 162.077
Angle α, β, γ (deg.)90.00, 103.61, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN B AND (RESSEQ 5:315 OR RESSEQ 401:401 )
211CHAIN A AND (RESSEQ 5:315 OR RESSEQ 401:401 )
311CHAIN C AND (RESSEQ 5:315 OR RESSEQ 401:401 )
411CHAIN D AND (RESSEQ 5:315 OR RESSEQ 401:401 )
511CHAIN E AND (RESSEQ 5:315 OR RESSEQ 401:401 )

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Components

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


Mass: 36277.723 Da / Num. of mol.: 5 / Fragment: UNP residues 43-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: glvI, glr4197 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta(DE3) pLysS / References: UniProt: Q7NDN8
#2: Chemical
ChemComp-RKE / (R)-ketamine / (2R)-2-(2-chlorophenyl)-2-(methylamino)cyclohexanone / Arketamine


Mass: 237.725 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H16ClNO / Comment: antagonist*YM
#3: Chemical
ChemComp-LMD / tetradecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside / n-Tetradecyl-b-D-maltopyranosid


Mass: 538.669 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H50O11
#4: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 5.3 Å3/Da / Density % sol: 76.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10-12% PEG 4000, 225 mM ammonium sulfate, 50 mM sodium acetate buffer (pH 3.9 - 4.1), VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.99→25 Å / Num. obs: 74604 / % possible obs: 97.6 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2
Reflection shellResolution: 2.99→3.15 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.2 / % possible all: 92.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3EAM

3eam


Resolution: 2.99→24.844 Å / SU ML: 0.37 / σ(F): 0 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 3452 5.04 %
Rwork0.1873 --
obs0.189 68525 89.77 %
all-74604 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.291 Å2 / ksol: 0.285 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-22.1538 Å20 Å2-36.5266 Å2
2---7.895 Å20 Å2
3----14.2587 Å2
Refinement stepCycle: LAST / Resolution: 2.99→24.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12625 0 675 58 13358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813641
X-RAY DIFFRACTIONf_angle_d1.22318582
X-RAY DIFFRACTIONf_dihedral_angle_d19.3855434
X-RAY DIFFRACTIONf_chiral_restr0.0722150
X-RAY DIFFRACTIONf_plane_restr0.0042230
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2541X-RAY DIFFRACTIONPOSITIONAL
12A2541X-RAY DIFFRACTIONPOSITIONAL0.042
13C2541X-RAY DIFFRACTIONPOSITIONAL0.042
14D2541X-RAY DIFFRACTIONPOSITIONAL0.038
15E2541X-RAY DIFFRACTIONPOSITIONAL0.04
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.03310.3942880.35671594X-RAY DIFFRACTION56
3.0331-3.07640.36111170.29142274X-RAY DIFFRACTION77
3.0764-3.12220.29251010.27452218X-RAY DIFFRACTION77
3.1222-3.17090.28891240.24212379X-RAY DIFFRACTION82
3.1709-3.22280.2691420.22922404X-RAY DIFFRACTION83
3.2228-3.27820.30621250.22142375X-RAY DIFFRACTION83
3.2782-3.33770.28371390.21552453X-RAY DIFFRACTION84
3.3377-3.40170.23921230.20882397X-RAY DIFFRACTION84
3.4017-3.4710.28781220.20622392X-RAY DIFFRACTION83
3.471-3.54630.23811340.20352594X-RAY DIFFRACTION89
3.5463-3.62850.23241370.19262655X-RAY DIFFRACTION93
3.6285-3.7190.23821470.19412712X-RAY DIFFRACTION94
3.719-3.81920.2031300.1882751X-RAY DIFFRACTION94
3.8192-3.93110.22071410.18842749X-RAY DIFFRACTION95
3.9311-4.05750.20681560.1852784X-RAY DIFFRACTION96
4.0575-4.20190.22021780.17342787X-RAY DIFFRACTION97
4.2019-4.36920.181460.15062816X-RAY DIFFRACTION97
4.3692-4.56690.16861400.13682738X-RAY DIFFRACTION95
4.5669-4.8060.13871460.12552802X-RAY DIFFRACTION97
4.806-5.10470.15831580.13512877X-RAY DIFFRACTION98
5.1047-5.49490.19021600.1482837X-RAY DIFFRACTION98
5.4949-6.04070.22861480.18552867X-RAY DIFFRACTION98
6.0407-6.89840.24941410.18792796X-RAY DIFFRACTION96
6.8984-8.63030.18361520.18112929X-RAY DIFFRACTION99
8.6303-24.84520.25061570.24032893X-RAY DIFFRACTION97

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