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- PDB-6hyr: THE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT Q193C+MMTS -

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Basic information

Entry
Database: PDB / ID: 6hyr
TitleTHE GLIC PENTAMERIC LIGAND-GATED ION CHANNEL MUTANT Q193C+MMTS
ComponentsProton-gated ion channel
KeywordsMEMBRANE 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
Proton-gated ion channel
Similarity search - Component
Biological speciesGloeobacter violaceus PCC 7421 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsHu, H.D. / Delarue, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel.
Authors: Hu, H. / Ataka, K. / Menny, A. / Fourati, Z. / Sauguet, L. / Corringer, P.J. / Koehl, P. / Heberle, J. / Delarue, M.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Jan 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)178,8266
Polymers178,3165
Non-polymers5111
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22450 Å2
ΔGint-146 kcal/mol
Surface area62940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.984, 128.285, 160.429
Angle α, β, γ (deg.)90.00, 100.96, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25B
16A
26C
17A
27D
18A
28E
19B
29C
110B
210D
111B
211E
112B
212C
113B
213D
114B
214E
115C
215D
116C
216E
117C
217D
118C
218E
119D
219E
120D
220E

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALARGARGAA5 - 1921 - 188
21VALVALARGARGBB5 - 1921 - 188
12VALVALARGARGAA5 - 1921 - 188
22VALVALARGARGCC5 - 1921 - 188
13VALVALARGARGAA5 - 1921 - 188
23VALVALARGARGDD5 - 1921 - 188
14VALVALARGARGAA5 - 1921 - 188
24VALVALARGARGEE5 - 1921 - 188
15TYRTYRPHEPHEAA194 - 315190 - 311
25TYRTYRPHEPHEBB194 - 315190 - 311
16TYRTYRPHEPHEAA194 - 315190 - 311
26TYRTYRPHEPHECC194 - 315190 - 311
17TYRTYRPHEPHEAA194 - 315190 - 311
27TYRTYRPHEPHEDD194 - 315190 - 311
18TYRTYRPHEPHEAA194 - 315190 - 311
28TYRTYRPHEPHEEE194 - 315190 - 311
19VALVALARGARGBB5 - 1921 - 188
29VALVALARGARGCC5 - 1921 - 188
110VALVALARGARGBB5 - 1921 - 188
210VALVALARGARGDD5 - 1921 - 188
111VALVALARGARGBB5 - 1921 - 188
211VALVALARGARGEE5 - 1921 - 188
112TYRTYRPHEPHEBB194 - 315190 - 311
212TYRTYRPHEPHECC194 - 315190 - 311
113TYRTYRPHEPHEBB194 - 315190 - 311
213TYRTYRPHEPHEDD194 - 315190 - 311
114TYRTYRPHEPHEBB194 - 315190 - 311
214TYRTYRPHEPHEEE194 - 315190 - 311
115VALVALARGARGCC5 - 1921 - 188
215VALVALARGARGDD5 - 1921 - 188
116VALVALARGARGCC5 - 1921 - 188
216VALVALARGARGEE5 - 1921 - 188
117TYRTYRPHEPHECC194 - 315190 - 311
217TYRTYRPHEPHEDD194 - 315190 - 311
118TYRTYRPHEPHECC194 - 315190 - 311
218TYRTYRPHEPHEEE194 - 315190 - 311
119VALVALARGARGDD5 - 1921 - 188
219VALVALARGARGEE5 - 1921 - 188
120TYRTYRPHEPHEDD194 - 315190 - 311
220TYRTYRPHEPHEEE194 - 315190 - 311

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20

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Components

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


Mass: 35663.148 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus PCC 7421 (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: isolated from a genetically manipulated source
Formula: C24H46O11 / Comment: detergent*YM
Has protein modificationY

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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: 5.07 Å3/Da / Density % sol: 75.74 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 12-14.5% PEG4K; 15% GLycerol; 400 mM NaSCN; 3% DMSO; 100mM NaAcetate pH 4.

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.5→49.73 Å / Num. obs: 39511 / % possible obs: 99.3 % / Redundancy: 3.1 % / Net I/σ(I): 6.4
Reflection shellResolution: 3.5→3.85 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.91 / SU B: 55.012 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1775 5 %RANDOM
Rwork0.231 ---
obs0.13542 33566 78.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 83.884 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å27.92 Å2
2---7.39 Å20 Å2
3---3.45 Å2
Refinement stepCycle: 1 / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12620 0 12 0 12632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212971
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212294
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.95917690
X-RAY DIFFRACTIONr_angle_other_deg1.08328297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.76151540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72322.87575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.062152065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2941590
X-RAY DIFFRACTIONr_chiral_restr0.1130.22075
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114065
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022865
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it13.2278.1676215
X-RAY DIFFRACTIONr_mcbond_other13.2228.1676214
X-RAY DIFFRACTIONr_mcangle_it18.43712.267730
X-RAY DIFFRACTIONr_mcangle_other18.43812.267731
X-RAY DIFFRACTIONr_scbond_it14.3748.8346756
X-RAY DIFFRACTIONr_scbond_other14.3738.8346757
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other19.21812.9829961
X-RAY DIFFRACTIONr_rigid_bond_restr1.942325256
X-RAY DIFFRACTIONr_sphericity_free17.98651
X-RAY DIFFRACTIONr_sphericity_bonded63.663524924
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A120420.04
12B120420.04
21A120880.02
22C120880.02
31A120860.02
32D120860.02
41A121000.03
42E121000.03
51A84740.02
52B84740.02
61A84720.03
62C84720.03
71A84720.02
72D84720.02
81A84820.01
82E84820.01
91B120340.04
92C120340.04
101B120460.04
102D120460.04
111B120460.04
112E120460.04
121B84940.01
122C84940.01
131B84980.01
132D84980.01
141B84760.02
142E84760.02
151C121080.02
152D121080.02
161C121940.02
162E121940.02
171C84940.01
172D84940.01
181C84900.02
182E84900.02
191D121120.03
192E121120.03
201D84760.02
202E84760.02
LS refinement shellResolution: 3.5→3.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 56 -
Rwork0.223 991 -
obs--32.76 %

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