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- PDB-4hfe: The GLIC pentameric Ligand-Gated Ion Channel F14'A ethanol-sensit... -

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Basic information

Entry
Database: PDB / ID: 4hfe
TitleThe GLIC pentameric Ligand-Gated Ion Channel F14'A ethanol-sensitive mutant complexed to ethanol
ComponentsProton-gated ion channel
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN / pentameric transmembrane channel / Ion-channel
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / extracellular ligand-gated monoatomic ion 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
ACETATE ION / ETHANOL / DIUNDECYL PHOSPHATIDYL CHOLINE / Unknown ligand / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSauguet, L. / Howard, R.J. / Malherbe, L. / Lee, U.S. / Corringer, P.J. / Harris, R.A. / Delarue, M.
CitationJournal: Nat Commun / Year: 2013
Title: Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel.
Authors: Sauguet, L. / Howard, R.J. / Malherbe, L. / Lee, U.S. / Corringer, P.J. / Harris, R.A. / Delarue, M.
History
DepositionOct 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: 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)188,46354
Polymers181,0785
Non-polymers7,38549
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38230 Å2
ΔGint-211 kcal/mol
Surface area61170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.990, 133.620, 159.130
Angle α, β, γ (deg.)90.00, 102.17, 90.00
Int Tables number5
Space group name H-MC121
Detailshomo-pentamer

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Components

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Protein / Sugars , 2 types, 11 molecules ABCDE

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


Mass: 36215.652 Da / Num. of mol.: 5 / Fragment: unp residues 44-359 / Mutation: F280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 C43 / References: UniProt: Q7NDN8
#6: 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

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Non-polymers , 7 types, 149 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O
#7: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#8: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 10 / Source method: obtained synthetically
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 5.2 Å3/Da / Density % sol: 73.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 12-15% PEG4K, 0.1M Na Acetate, 0.4M NaSCN, 0.2M Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9194 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2011
Details: Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 2.8→49.5 Å / Num. obs: 90680 / % possible obs: 99.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 74.01 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.047 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.407 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.9022 / Cor.coef. Fo:Fc free: 0.8963 / SU R Cruickshank DPI: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4537 5.01 %RANDOM
Rwork0.205 ---
obs0.2055 90624 99.52 %-
Displacement parametersBiso mean: 86.33 Å2
Baniso -1Baniso -2Baniso -3
1--6.2907 Å20 Å220.041 Å2
2---8.737 Å20 Å2
3---15.0278 Å2
Refine analyzeLuzzati coordinate error obs: 0.419 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12595 0 430 106 13131
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913346HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0518140HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6099SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes265HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1900HARMONIC5
X-RAY DIFFRACTIONt_it13346HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion3.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1770SEMIHARMONIC5
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_contact14963SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2469 365 5.48 %
Rwork0.2443 6295 -
all0.2444 6660 -
obs--99.52 %
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)
11.4544-0.25460.93810.6714-0.35212.5636-0.02250.03560.1695-0.08820.00910.0815-0.3719-0.36320.01340.06960.1622-0.1504-0.154-0.0168-0.15839.8703-6.566729.6429
20.31840.0370.48190.4964-0.20740.77910.01790.0367-0.03010.0369-0.0196-0.0053-0.0852-0.01680.0016-0.03570.00020.0758-0.1419-0.04770.028558.4688-26.740548.4559
32.31990.19332.48060.57170.32083.83290.097-0.0107-0.05060.0229-0.05740.17880.0384-0.3932-0.0396-0.15950.0532-0.08190.074-0.0312-0.134827.963-28.019335.6983
41.22450.30951.35260.77360.56793.18840.11980.1072-0.2148-0.0918-0.04930.13590.2829-0.0748-0.0705-0.01550.0523-0.1798-0.1022-0.0824-0.078742.0882-47.685728.5732
51.1380.17261.22270.76910.28874.5684-0.01830.2576-0.1073-0.2169-0.0213-0.0679-0.08690.24920.0396-0.05930.1429-0.0746-0.0583-0.1-0.166462.9496-38.398617.6423
60.9099-0.18491.1220.8149-0.74493.7603-0.06440.16140.167-0.1794-0.0359-0.1172-0.17620.1080.10030.0555-0.0011-0.0856-0.10340.0497-0.165461.5756-13.022918.3867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|315 }A5 - 315
2X-RAY DIFFRACTION2{ A|411 - A|412 C|406 - C|407 B|408 - B|409 E|406 - E|407 D|408 - D|409 }A411 - 412
3X-RAY DIFFRACTION2{ A|411 - A|412 C|406 - C|407 B|408 - B|409 E|406 - E|407 D|408 - D|409 }C406 - 407
4X-RAY DIFFRACTION2{ A|411 - A|412 C|406 - C|407 B|408 - B|409 E|406 - E|407 D|408 - D|409 }B408 - 409
5X-RAY DIFFRACTION2{ A|411 - A|412 C|406 - C|407 B|408 - B|409 E|406 - E|407 D|408 - D|409 }E406 - 407
6X-RAY DIFFRACTION2{ A|411 - A|412 C|406 - C|407 B|408 - B|409 E|406 - E|407 D|408 - D|409 }D408 - 409
7X-RAY DIFFRACTION3{ B|5 - B|315 }B5 - 315
8X-RAY DIFFRACTION4{ C|5 - C|315 }C5 - 315
9X-RAY DIFFRACTION5{ D|5 - D|315 }D5 - 315
10X-RAY DIFFRACTION6{ E|5 - E|315 }E5 - 315

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