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- PDB-4lmk: GLIC Liganded-closed-channel Conformation, Mutant Y27'A -

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Basic information

Entry
Database: PDB / ID: 4lmk
TitleGLIC Liganded-closed-channel Conformation, Mutant Y27'A
ComponentsProton-gated ion channel
KeywordsTRANSPORT PROTEIN / pentameric ligand-gated ion channel / membrane protein / prokaryotic CYS-loop receptor
Function / homology
Function and homology information


sodium channel activity / potassium channel activity / transmembrane transporter complex / 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: 3.22 Å
AuthorsGrosman, C. / Gonzalez-Gutierrez, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Gating of the proton-gated ion channel from Gloeobacter violaceus at pH 4 as revealed by X-ray crystallography.
Authors: Gonzalez-Gutierrez, G. / Cuello, L.G. / Nair, S.K. / Grosman, C.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / 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 / _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 / _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
E: Proton-gated ion channel
C: Proton-gated ion channel
B: Proton-gated ion channel
D: Proton-gated ion channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,16616
Polymers181,3645
Non-polymers80311
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23430 Å2
ΔGint-239 kcal/mol
Surface area63570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.990, 134.280, 159.940
Angle α, β, γ (deg.)90.000, 102.060, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 7:316 )
21chain E and (resseq 7:316 )
31chain C and (resseq 7:316 )
41chain B and (resseq 7:316 )
51chain D and (resseq 7:316 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 7 - 316 / Label seq-ID: 9 - 318

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A' and (resseq 7:316 )AA
2chain 'E' and (resseq 7:316 )EB
3chain 'C' and (resseq 7:316 )CC
4chain 'B' and (resseq 7:316 )BD
5chain 'D' and (resseq 7:316 )DE

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Components

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


Mass: 36272.711 Da / Num. of mol.: 5 / Fragment: UNP residues 44-359 / Mutation: T293A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glvI, glr4197 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7NDN8
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na

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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: 5.24 Å3/Da / Density % sol: 76.5 %
Description: RPIM = 0.113 (0.700 FOR HIGHEST RESOLUTION SHELL)
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 10-12% PEG4000, 225 mM ammonium sulfate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 20, 2012
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.22→49.27 Å / Num. obs: 39396 / % possible obs: 98.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 47.21 Å2 / Rmerge(I) obs: 0.206 / Net I/σ(I): 8.4
Reflection shellHighest resolution: 3.22 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.268 / Mean I/σ(I) obs: 1.2 / % possible all: 85.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EHZ

3ehz


Resolution: 3.22→48.761 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 0.11 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 1953 4.96 %
Rwork0.2108 --
obs0.2121 39347 64.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.58 Å2 / Biso mean: 46.1502 Å2 / Biso min: 2.37 Å2
Refinement stepCycle: LAST / Resolution: 3.22→48.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12570 0 22 0 12592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112916
X-RAY DIFFRACTIONf_angle_d1.37817640
X-RAY DIFFRACTIONf_chiral_restr0.1022060
X-RAY DIFFRACTIONf_plane_restr0.0062210
X-RAY DIFFRACTIONf_dihedral_angle_d15.8944619
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2514X-RAY DIFFRACTIONTORSIONAL0.051
12E2514X-RAY DIFFRACTIONTORSIONAL0.051
13C2514X-RAY DIFFRACTIONTORSIONAL0.047
14B2514X-RAY DIFFRACTIONTORSIONAL0.056
15D2514X-RAY DIFFRACTIONTORSIONAL0.055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.22-3.30080.5043320.36156159314
3.3008-3.39010.3563320.293774677818
3.3901-3.48980.3551550.28586091521
3.4898-3.60240.2693620.2571182124429
3.6024-3.73110.3134780.25071538161637
3.7311-3.88040.27631310.24432135226653
3.8804-4.0570.2721560.23232968312472
4.057-4.27070.2272000.18823559375987
4.2707-4.53810.22191950.17823827402293
4.5381-4.88820.17161980.14773883408194
4.8882-5.37960.19662080.17073976418496
5.3796-6.15670.24652040.21213973417797
6.1567-7.75180.26761930.25024068426198
7.7518-48.76650.23762090.24424118432797

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