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- PDB-6ssi: Structure of the pentameric ligand-gated ion channel ELIC in comp... -

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Basic information

Entry
Database: PDB / ID: 6ssi
TitleStructure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody
Components
  • Cys-loop ligand-gated ion channel
  • NANOBODY 22
KeywordsTRANSPORT PROTEIN / ION CHANNEL / CYS-LOOP RECEPTOR / PENTAMERIC LIGAND GATED ION CHANNEL / LGIC / ELIC / NANOBODY
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
GAMMA-AMINO-BUTANOIC ACID / ACETATE ION / Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsUlens, C. / Brams, M. / Evans, G.L. / Spurny, R. / Govaerts, C. / Pardon, E. / Steyaert, J.
Funding support Belgium, 5items
OrganizationGrant numberCountry
Research Foundation - Flanders1200261 Belgium
Research Foundation - FlandersG.0762.13 Belgium
KU LeuvenOT/13/095 Belgium
KU LeuvenC32/16/035 Belgium
KU LeuvenC14/17/093 Belgium
CitationJournal: Elife / Year: 2020
Title: Modulation of the Erwinia ligand-gated ion channel (ELIC) and the 5-HT 3 receptor via a common vestibule site.
Authors: Brams, M. / Govaerts, C. / Kambara, K. / Price, K.L. / Spurny, R. / Gharpure, A. / Pardon, E. / Evans, G.L. / Bertrand, D. / Lummis, S.C. / Hibbs, R.E. / Steyaert, J. / Ulens, C.
History
DepositionSep 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 22
G: NANOBODY 22
H: NANOBODY 22
I: NANOBODY 22
J: NANOBODY 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,53442
Polymers248,91210
Non-polymers5,62332
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42980 Å2
ΔGint-212 kcal/mol
Surface area85600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.604, 146.563, 140.242
Angle α, β, γ (deg.)90.000, 111.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Antibody , 2 types, 10 molecules ABCDEFGHIJ

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


Mass: 36465.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#2: Antibody
NANOBODY 22


Mass: 13316.725 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)

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Non-polymers , 8 types, 177 molecules

#3: Chemical
ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO2
#4: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical
ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 4.27 Å3/Da / Density % sol: 71.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M GABA, 0.2 M Ca(OAc)2, 0.1 M MES buffer, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.58→49.35 Å / Num. obs: 123740 / % possible obs: 99.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 87.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.035 / Rrim(I) all: 0.077 / Net I/σ(I): 13.4 / Num. measured all: 594559
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.58-2.634.61.3942695757990.4580.7191.572195.2
14.16-49.354.30.02731777440.9990.0140.0314593.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
MxCuBEdata collection
XDSMar 15, 2019data reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vl0, 3p0g

2vl0

3p0g


Resolution: 2.59→47.06 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.306 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.235
RfactorNum. reflection% reflectionSelection details
Rfree0.246 6188 5 %RANDOM
Rwork0.23 ---
obs0.231 123710 99.8 %-
Displacement parametersBiso max: 167.99 Å2 / Biso mean: 77.43 Å2 / Biso min: 36.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.9344 Å20 Å22.5217 Å2
2--9.4869 Å20 Å2
3----7.5524 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: final / Resolution: 2.59→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16423 0 356 145 16924
Biso mean--101.57 61.9 -
Num. residues----2081
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5834SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2868HARMONIC5
X-RAY DIFFRACTIONt_it17176HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2288SEMIHARMONIC5
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_contact19025SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d17176HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg23331HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion15.26
LS refinement shellResolution: 2.59→2.6 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3329 124 5.01 %
Rwork0.2784 2351 -
all0.2809 2475 -
obs--94.43 %

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