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- PDB-6hjy: X-ray structure of a pentameric ligand gated ion channel from Erw... -

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Basic information

Entry
Database: PDB / ID: 6hjy
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) Delta8 truncation mutant in complex with nanobody 72
Components
  • (Cys-loop ligand-gated ion ...) x 4
  • (nanobody 72) x 2
KeywordsMEMBRANE PROTEIN / ion channel / pentameric ligand-gated ion channel / cya-loop receptor
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / 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 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
Similarity search - Domain/homology
Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsSpurny, R. / Govaerts, C. / Evans, G.L. / Pardon, E. / Steyaert, J. / Ulens, C.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: A lipid site shapes the agonist response of a pentameric ligand-gated ion channel.
Authors: Henault, C.M. / Govaerts, C. / Spurny, R. / Brams, M. / Estrada-Mondragon, A. / Lynch, J. / Bertrand, D. / Pardon, E. / Evans, G.L. / Woods, K. / Elberson, B.W. / Cuello, L.G. / Brannigan, G. ...Authors: Henault, C.M. / Govaerts, C. / Spurny, R. / Brams, M. / Estrada-Mondragon, A. / Lynch, J. / Bertrand, D. / Pardon, E. / Evans, G.L. / Woods, K. / Elberson, B.W. / Cuello, L.G. / Brannigan, G. / Nury, H. / Steyaert, J. / Baenziger, J.E. / Ulens, C.
History
DepositionSep 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / 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
Revision 1.2Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: 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: Cys-loop ligand-gated ion channel
B: Cys-loop ligand-gated ion channel
C: Cys-loop ligand-gated ion channel
D: Cys-loop ligand-gated ion channel
E: Cys-loop ligand-gated ion channel
F: nanobody 72
G: nanobody 72
H: nanobody 72
I: nanobody 72
J: nanobody 72


Theoretical massNumber of molelcules
Total (without water)227,63410
Polymers227,63410
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35890 Å2
ΔGint-139 kcal/mol
Surface area79770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.675, 155.093, 101.618
Angle α, β, γ (deg.)90.000, 103.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Cys-loop ligand-gated ion ... , 4 types, 5 molecules ABCDE

#1: Protein Cys-loop ligand-gated ion channel / ELIC


Mass: 32102.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#2: Protein Cys-loop ligand-gated ion channel / ELIC


Mass: 32413.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#3: Protein Cys-loop ligand-gated ion channel / ELIC


Mass: 32031.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#4: Protein Cys-loop ligand-gated ion channel / ELIC


Mass: 32217.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7

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Antibody , 2 types, 5 molecules FJGHI

#5: Antibody nanobody 72


Mass: 13367.960 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#6: Antibody nanobody 72


Mass: 13239.831 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 300 mM ammonium formate, 50 mM TRIS pH 9.0 and 33% PEG monomethylether 550

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9754 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2.78→49.49 Å / Num. obs: 71824 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 88.12 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.094 / Rrim(I) all: 0.136 / Net I/av σ(I): 6.6 / Net I/σ(I): 6.6
Reflection shellResolution: 2.78→2.85 Å / Rmerge(I) obs: 1.442 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4318 / CC1/2: 0.281 / Rpim(I) all: 1.379 / Rrim(I) all: 1.998

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HJX

6hjx


Resolution: 2.78→49.49 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.712 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.307
RfactorNum. reflection% reflectionSelection details
Rfree0.233 3602 5.02 %RANDOM
Rwork0.225 ---
obs0.226 71790 99 %-
Displacement parametersBiso max: 253.68 Å2 / Biso mean: 101.39 Å2 / Biso min: 45.07 Å2
Baniso -1Baniso -2Baniso -3
1-21.464 Å20 Å2-6.2316 Å2
2---10.5398 Å20 Å2
3----10.9242 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 2.78→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16066 0 0 0 16066
Num. residues----2006
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5557SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes395HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2408HARMONIC5
X-RAY DIFFRACTIONt_it16497HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2113SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17956SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d16497HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg22427HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion17.24
LS refinement shellResolution: 2.78→2.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2296 246 5.13 %
Rwork0.2403 4553 -
all0.2397 4799 -
obs--89.42 %

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