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- PDB-2yn6: Pentameric Ligand-Gated Ion Channel ELIC in Complex with Barium -

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Basic information

Entry
Database: PDB / ID: 2yn6
TitlePentameric Ligand-Gated Ion Channel ELIC in Complex with Barium
ComponentsPENTAMERIC LIGAND-GATED ION CHANNEL ELIC
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / CATION SELECTIVE ION CHANNEL / PROKARYOTIC CYS-LOOP RECEPTOR
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / identical protein binding / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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 ...Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / 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
: / Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDICKEYA DADANTII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsZimmermann, I. / Marabelli, A. / Bertozzi, C. / Sivilotti, L.G. / Dutzler, R.
CitationJournal: Plos Biol. / Year: 2012
Title: Inhibition of the Prokaryotic Pentameric Ligand-Gated Ion Channel Elic by Divalent Cations.
Authors: Zimmermann, I. / Marabelli, A. / Bertozzi, C. / Sivilotti, L.G. / Dutzler, R.
History
DepositionOct 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PENTAMERIC LIGAND-GATED ION CHANNEL ELIC
B: PENTAMERIC LIGAND-GATED ION CHANNEL ELIC
C: PENTAMERIC LIGAND-GATED ION CHANNEL ELIC
D: PENTAMERIC LIGAND-GATED ION CHANNEL ELIC
E: PENTAMERIC LIGAND-GATED ION CHANNEL ELIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,04317
Polymers184,3955
Non-polymers1,64812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27250 Å2
ΔGint-219.7 kcal/mol
Surface area66890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.473, 100.473, 263.951
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.3127, 0.2151, 0.9252), (-0.1781, 0.97, -0.1653), (-0.933, -0.1131, 0.3416)31.5155, 0.65, -0.4879
2given(0.7998, 0.1791, 0.5729), (-0.0691, 0.9206, -0.3843), (-0.5962, -0.347, -0.724)-41.1444, 7.2234, 28.3112
3given(0.8097, -0.0728, -0.5823), (0.1748, 0.9174, -0.3576), (0.5602, -0.3913, -0.7301)-16.4662, 10.6351, 46.2978
4given(0.2887, -0.1862, -0.9391), (0.2183, 0.9679, -0.1248), (0.9322, -0.169, 0.32)8.6561, 6.5591, 30.048

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Components

#1: Protein
PENTAMERIC LIGAND-GATED ION CHANNEL ELIC


Mass: 36879.000 Da / Num. of mol.: 5 / Fragment: RESIDUES 22-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICKEYA DADANTII (bacteria) / Strain: 3937 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E0SJQ4
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ba

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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: 3.6 Å3/Da / Density % sol: 65 %
Description: STARTING MODEL 2VL0 WAS MISSING THE RESIDUE GLYCINE 164. CORRECTED IN THIS STRUCTURE
Crystal growpH: 6.5 / Details: 50 MM ADA PH6.5, 50 MM BAAC2, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.4
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 38612 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 84.26 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.1
Reflection shellResolution: 3.3→3.5 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.7 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL0

2vl0


Resolution: 3.31→19.986 Å / SU ML: 0.45 / σ(F): 1.35 / Phase error: 27.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 1926 5 %
Rwork0.227 --
obs0.2285 38410 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.31→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12525 0 12 0 12537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812865
X-RAY DIFFRACTIONf_angle_d1.21817535
X-RAY DIFFRACTIONf_dihedral_angle_d15.9054615
X-RAY DIFFRACTIONf_chiral_restr0.0761950
X-RAY DIFFRACTIONf_plane_restr0.0052235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3098-3.39220.33391360.31142378X-RAY DIFFRACTION91
3.3922-3.48340.35261440.29052625X-RAY DIFFRACTION100
3.4834-3.58540.33711290.28092634X-RAY DIFFRACTION100
3.5854-3.70040.28531510.27172579X-RAY DIFFRACTION100
3.7004-3.83180.29571350.25962612X-RAY DIFFRACTION100
3.8318-3.9840.27781260.24782631X-RAY DIFFRACTION100
3.984-4.16380.27171530.24522632X-RAY DIFFRACTION100
4.1638-4.38110.2891320.21922596X-RAY DIFFRACTION100
4.3811-4.65240.23231340.20082619X-RAY DIFFRACTION100
4.6524-5.00640.26371390.2042637X-RAY DIFFRACTION100
5.0064-5.50060.23711380.20822616X-RAY DIFFRACTION100
5.5006-6.27490.27051380.21982655X-RAY DIFFRACTION100
6.2749-7.8260.23931330.23562617X-RAY DIFFRACTION100
7.826-19.9860.18171380.18822653X-RAY DIFFRACTION100

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