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

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Basic information

Entry
Database: PDB / ID: 6hjx
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) 7'C pore mutant (L238C) in complex with nanobody 72
Components
  • (Cys-loop ligand-gated ion ...) x 5
  • nanobody 72Single-domain antibody
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 / transmembrane signaling receptor activity / 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
PHOSPHATIDYLETHANOLAMINE / Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,24122
Polymers244,60610
Non-polymers4,63512
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, ...
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41900 Å2
ΔGint-136 kcal/mol
Surface area82920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.251, 156.277, 102.496
Angle α, β, γ (deg.)90.000, 102.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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

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


Mass: 35244.055 Da / Num. of mol.: 1 / Mutation: C300S, C313S, L238C
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: 35555.391 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
#3: Protein Cys-loop ligand-gated ion channel / ELIC


Mass: 35880.832 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: 35726.695 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
#5: Protein Cys-loop ligand-gated ion channel / ELIC


Mass: 35359.141 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 / Sugars , 2 types, 10 molecules FGHIJ

#6: Antibody
nanobody 72 / Single-domain antibody


Mass: 13367.960 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#9: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 5 types, 315 molecules

#7: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE / Phosphatidylethanolamine


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#10: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MES (pH 6.5) and 30% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91958 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91958 Å / Relative weight: 1
ReflectionResolution: 2.5→48.84 Å / Num. obs: 101800 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Net I/av σ(I): 14.8 / Net I/σ(I): 14.8
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.948 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 14853 / CC1/2: 0.475 / Rpim(I) all: 0.607 / Rrim(I) all: 1.128

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yoe

2yoe


Resolution: 2.5→47.587 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2451 5067 4.98 %
Rwork0.2042 96669 -
obs0.2063 101736 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.93 Å2 / Biso mean: 59.4485 Å2 / Biso min: 22.64 Å2
Refinement stepCycle: final / Resolution: 2.5→47.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16540 0 302 308 17150
Biso mean--85.15 51.95 -
Num. residues----2131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.52840.37431820.33063235100
2.5284-2.55820.35781440.30813223100
2.5582-2.58940.36991530.30993231100
2.5894-2.62220.36761630.29663196100
2.6222-2.65670.35591670.29893204100
2.6567-2.6930.32961650.29113246100
2.693-2.73150.33711680.27823193100
2.7315-2.77230.30791590.26883218100
2.7723-2.81560.32131690.27043225100
2.8156-2.86180.32221570.26513223100
2.8618-2.91110.33441490.25733231100
2.9111-2.9640.29621730.25513214100
2.964-3.0210.31051850.26213238100
3.021-3.08270.32141760.24553185100
3.0827-3.14970.28021830.23243202100
3.1497-3.22290.30161580.23353268100
3.2229-3.30350.25711800.23293200100
3.3035-3.39280.25121780.22123209100
3.3928-3.49260.29221890.21683175100
3.4926-3.60530.27241700.22173226100
3.6053-3.73410.28041630.20193219100
3.7341-3.88360.25381530.19283243100
3.8836-4.06020.22071530.17893228100
4.0602-4.27420.19881840.17073223100
4.2742-4.54180.17732170.15343174100
4.5418-4.89210.16521540.14873253100
4.8921-5.38380.19791740.1663266100
5.3838-6.16150.24211640.18413225100
6.1615-7.75730.22361760.19153239100
7.7573-470.19821610.1776325798

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