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

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Basic information

Entry
Database: PDB / ID: 6ssp
TitleStructure of the pentameric ligand-gated ion channel ELIC in complex with a NAM nanobody
Components
  • Cys-loop ligand-gated ion channel
  • NANOBODY 21Single-domain antibody
KeywordsTRANSPORT PROTEIN / ELIC / CYS-LOOP RECEPTOR / NANOBODY / PENTAMERIC LIGAND GATED ION CHANNEL
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
Cys-loop ligand-gated ion channel
Similarity search - Component
Biological speciesDickeya chrysanthemi (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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 9, 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 / Derived calculations / Category: citation / struct_conn
Item: _citation.title / _struct_conn.pdbx_dist_value ..._citation.title / _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
Revision 1.3Jan 24, 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: Cys-loop ligand-gated ion channel
G: Cys-loop ligand-gated ion channel
H: Cys-loop ligand-gated ion channel
I: Cys-loop ligand-gated ion channel
J: Cys-loop ligand-gated ion channel
K: NANOBODY 21
L: NANOBODY 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,44430
Polymers395,15712
Non-polymers5,28718
Water0
1
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
K: NANOBODY 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,22215
Polymers197,5796
Non-polymers2,6439
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Cys-loop ligand-gated ion channel
G: Cys-loop ligand-gated ion channel
H: Cys-loop ligand-gated ion channel
I: Cys-loop ligand-gated ion channel
J: Cys-loop ligand-gated ion channel
L: NANOBODY 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,22215
Polymers197,5796
Non-polymers2,6439
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.804, 122.354, 128.221
Angle α, β, γ (deg.)71.020, 64.190, 61.660
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 36465.578 Da / Num. of mol.: 10
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 21 / Single-domain antibody


Mass: 15250.717 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)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
Has ligand of interestN

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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: 3.99 Å3/Da / Density % sol: 69.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Na2SO4, 0.1 M bis-trispropane, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→48.32 Å / Num. obs: 82177 / % possible obs: 89.8 % / Redundancy: 1.8 % / Biso Wilson estimate: 105.94 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.053 / Rrim(I) all: 0.074 / Net I/σ(I): 5.6 / Num. measured all: 146197
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
3.25-3.421.70.8071360080450.4830.8071.1410.760.3
10.27-48.321.90.017535728120.9910.0170.02418.597.3

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Processing

Software
NameVersionClassification
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
MOLREPphasing
PHENIX1.16-3549refinement
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vl0, 3p0g

2vl0

3p0g


Resolution: 3.25→48.32 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.474
RfactorNum. reflection% reflectionSelection details
Rfree0.264 4085 4.97 %RANDOM
Rwork0.248 ---
obs0.249 82174 89.9 %-
Displacement parametersBiso max: 241.96 Å2 / Biso mean: 104.73 Å2 / Biso min: 46.74 Å2
Baniso -1Baniso -2Baniso -3
1--2.3709 Å21.5816 Å23.2684 Å2
2--2.4382 Å20.8879 Å2
3----0.0673 Å2
Refine analyzeLuzzati coordinate error obs: 0.56 Å
Refinement stepCycle: final / Resolution: 3.25→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25905 0 328 0 26233
Biso mean--138.67 --
Num. residues----3260
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8899SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4482HARMONIC5
X-RAY DIFFRACTIONt_it26939HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion3650SEMIHARMONIC5
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_contact30430SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d26939HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg36771HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion17.29
LS refinement shellResolution: 3.25→3.29 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2537 67 4.08 %
Rwork0.2502 1577 -
all0.2503 1644 -
obs--50.46 %

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