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- PDB-5v6o: Crystal Structure of the highly open channel-stabilized mutant G-... -

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Basic information

Entry
Database: PDB / ID: 5v6o
TitleCrystal Structure of the highly open channel-stabilized mutant G-2'I + I9'A of GLIC
ComponentsProton-gated ion channel
Keywordsmembrane protein / metal transport / GLIC / Cys-loop receptors / ion channel / GluCl / ELIC
Function / homology
Function and homology information


sodium channel activity / transmembrane transporter complex / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.121 Å
AuthorsGonzalez-Gutierrez, G. / Grosman, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01-NS042169 United States
CitationJournal: J. Gen. Physiol. / Year: 2017
Title: Chasing the open-state structure of pentameric ligand-gated ion channels.
Authors: Gonzalez-Gutierrez, G. / Wang, Y. / Cymes, G.D. / Tajkhorshid, E. / Grosman, C.
History
DepositionMar 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: Proton-gated ion channel
E: Proton-gated ion channel
C: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,74927
Polymers177,5255
Non-polymers4,22522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27010 Å2
ΔGint-260 kcal/mol
Surface area63560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.388, 133.338, 160.312
Angle α, β, γ (deg.)90.000, 101.770, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA8 - 323
211chain BB8 - 321
311chain CC8 - 321
411chain DD8 - 321
511chain EE8 - 321

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Components

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


Mass: 35504.910 Da / Num. of mol.: 5 / Fragment: unp residues 50-359 / Mutation: C27S, K33C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria)
Strain: PCC 7421 / 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.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4

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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: 5.26 Å3/Da / Density % sol: 76.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Sodium Acetate 50 mM pH 3.9-4.2 Ammonium Sulfate 200-250 mM PEG 4000 10-12%
PH range: 3.9-4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.121→105.979 Å / Num. obs: 65357 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 66.78 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.089 / Rrim(I) all: 0.186 / Net I/σ(I): 8.7 / Num. measured all: 276516
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
3.121-3.1324.31.090.7640.6021.24899.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EHZ

3ehz


Resolution: 3.121→70.443 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.59
RfactorNum. reflection% reflection
Rfree0.2795 3249 4.98 %
Rwork0.2403 --
obs0.2423 65223 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.87 Å2 / Biso mean: 67.4838 Å2 / Biso min: 38.1 Å2
Refinement stepCycle: final / Resolution: 3.121→70.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12583 0 128 0 12711
Biso mean--82.81 --
Num. residues----1550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113029
X-RAY DIFFRACTIONf_angle_d1.54917776
X-RAY DIFFRACTIONf_chiral_restr0.0652060
X-RAY DIFFRACTIONf_plane_restr0.0082208
X-RAY DIFFRACTIONf_dihedral_angle_d14.3024662
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7322X-RAY DIFFRACTION7.702TORSIONAL
12B7322X-RAY DIFFRACTION7.702TORSIONAL
13C7322X-RAY DIFFRACTION7.702TORSIONAL
14D7322X-RAY DIFFRACTION7.702TORSIONAL
15E7322X-RAY DIFFRACTION7.702TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1212-3.16780.45011510.387827002851100
3.1678-3.21730.43441460.379926462792100
3.2173-3.270.42161390.35952705284499
3.27-3.32640.38481300.34412655278599
3.3264-3.38690.34411430.316527012844100
3.3869-3.45210.33361200.29712688280899
3.4521-3.52250.32351420.284326822824100
3.5225-3.59910.32931560.269627002856100
3.5991-3.68280.34641420.270126372779100
3.6828-3.77490.31421370.260926902827100
3.7749-3.8770.33121300.2527182848100
3.877-3.99110.30681530.240726882841100
3.9911-4.11990.24981580.212126702828100
4.1199-4.26710.22151450.202927072852100
4.2671-4.43790.25551600.205726582818100
4.4379-4.63990.24191280.18127052833100
4.6399-4.88440.2111450.172526822827100
4.8844-5.19040.22061570.17626782835100
5.1904-5.5910.24651680.203627042872100
5.591-6.15330.27781410.217327142855100
6.1533-7.0430.26151320.220627222854100
7.043-8.87070.24251120.22527572869100
8.8707-70.46050.24151140.25772767288198

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