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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 / 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
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

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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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 192
2010B5 - 192
1020A5 - 192
2020C5 - 192
1030A5 - 192
2030D5 - 192
1040A5 - 192
2040E5 - 192
1050A194 - 315
2050B194 - 315
1060A194 - 315
2060C194 - 315
1070A194 - 315
2070D194 - 315
1080A194 - 315
2080E194 - 315
1090B5 - 192
2090C5 - 192
10100B5 - 192
20100D5 - 192
10110B5 - 192
20110E5 - 192
10120B194 - 315
20120C194 - 315
10130B194 - 315
20130D194 - 315
10140B194 - 315
20140E194 - 315
10150C5 - 192
20150D5 - 192
10160C5 - 192
20160E5 - 192
10170C194 - 315
20170D194 - 315
10180C194 - 315
20180E194 - 315
10190D5 - 192
20190E5 - 192
10200D194 - 315
20200E194 - 315

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

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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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