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- PDB-4hfh: The GLIC pentameric Ligand-Gated Ion Channel (wild-type) complexe... -

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Basic information

Entry
Database: PDB / ID: 4hfh
TitleThe GLIC pentameric Ligand-Gated Ion Channel (wild-type) complexed to bromoform
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 / TRIBROMOMETHANE / DIUNDECYL PHOSPHATIDYL CHOLINE / Unknown ligand / Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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)194,23263
Polymers181,4595
Non-polymers12,77358
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41940 Å2
ΔGint-238 kcal/mol
Surface area61090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.000, 132.650, 159.270
Angle α, β, γ (deg.)90.00, 102.16, 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: 36291.750 Da / Num. of mol.: 5
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
#7: 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, 322 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C32H65NO8P / Comment: phospholipid*YM
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 10 / Source method: obtained synthetically
#5: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#8: Chemical
ChemComp-MBR / TRIBROMOMETHANE


Mass: 252.731 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CHBr3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 5.15 Å3/Da / Density % sol: 76.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 12-15% PEG4K, 0.1M Na Acetate, 0.4M NaSCN, 2% bromoform, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9191 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 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: 0.9191 Å / Relative weight: 1
ReflectionResolution: 2.65→49.1 Å / Num. obs: 105994 / % possible obs: 99.1 % / Redundancy: 8.8 % / Biso Wilson estimate: 72.57 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.042 / Net I/σ(I): 15
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.474 / % possible all: 96.1

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→21.71 Å / Cor.coef. Fo:Fc: 0.9174 / Cor.coef. Fo:Fc free: 0.9128 / SU R Cruickshank DPI: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 5282 4.98 %RANDOM
Rwork0.202 ---
obs0.2025 105994 99.47 %-
Displacement parametersBiso mean: 74.09 Å2
Baniso -1Baniso -2Baniso -3
1--10.0112 Å20 Å219.9296 Å2
2--1.6486 Å20 Å2
3---8.3626 Å2
Refine analyzeLuzzati coordinate error obs: 0.378 Å
Refinement stepCycle: LAST / Resolution: 2.65→21.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12625 0 514 270 13409
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00913552HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0518395HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6227SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes275HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1927HARMONIC5
X-RAY DIFFRACTIONt_it13552HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion3.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1781SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies21HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15569SEMIHARMONIC4
LS refinement shellResolution: 2.65→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2771 373 4.85 %
Rwork0.2467 7313 -
all0.2481 7686 -
obs--99.47 %
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)
10.8316-0.15850.83010.4769-0.25611.8121-0.0055-0.07720.0742-0.00070.03610.0294-0.126-0.1772-0.03060.07870.0521-0.0865-0.12320.0113-0.121840.2032-6.349729.7027
21.89140.13692.00610.42810.22282.92180.0433-0.0422-0.05980.0413-0.01420.0986-0.0049-0.1597-0.0291-0.09580.0103-0.0254-0.0134-0.0025-0.106728.0927-27.509635.8064
30.86960.18281.01540.49640.44532.36290.04710.0256-0.15540.0093-0.01830.04470.112-0.0147-0.02880.04410.0079-0.1173-0.1455-0.025-0.064641.9025-47.253928.8315
40.67390.09970.80960.51910.4032.77580.00890.0592-0.092-0.12230.0176-0.0592-0.06370.17-0.02660.01550.0317-0.0603-0.1149-0.0328-0.109962.8411-38.271217.8404
50.7189-0.18160.94240.5473-0.50652.8019-0.01020.02040.1245-0.1015-0.051-0.0994-0.06130.06570.06120.0636-0.0177-0.0554-0.150.0279-0.11261.8164-12.981418.5326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|315 }A5 - 315
2X-RAY DIFFRACTION2{ B|5 - B|315 }B5 - 315
3X-RAY DIFFRACTION3{ C|5 - C|315 }C5 - 315
4X-RAY DIFFRACTION4{ D|5 - D|315 }D5 - 315
5X-RAY DIFFRACTION5{ E|5 - E|315 }E5 - 315

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