[English] 日本語
Yorodumi
- PDB-5lg3: X-ray structure of a pentameric ligand gated ion channel from Erw... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lg3
TitleX-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with chlorpromazine
ComponentsGamma-aminobutyric-acid receptor subunit beta-1
KeywordsTRANSPORT PROTEIN / Ion channel / MEMBRANE PROTEIN
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 / 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
Chem-Z80 / Gamma-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.567 Å
AuthorsNys, M. / Wijckmans, E. / Farinha, A. / Brams, M. / Spurny, R. / Ulens, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Allosteric binding site in a Cys-loop receptor ligand-binding domain unveiled in the crystal structure of ELIC in complex with chlorpromazine.
Authors: Nys, M. / Wijckmans, E. / Farinha, A. / Yoluk, O. / Andersson, M. / Brams, M. / Spurny, R. / Peigneur, S. / Tytgat, J. / Lindahl, E. / Ulens, C.
History
DepositionJul 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 7, 2022Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-aminobutyric-acid receptor subunit beta-1
B: Gamma-aminobutyric-acid receptor subunit beta-1
C: Gamma-aminobutyric-acid receptor subunit beta-1
D: Gamma-aminobutyric-acid receptor subunit beta-1
E: Gamma-aminobutyric-acid receptor subunit beta-1
F: Gamma-aminobutyric-acid receptor subunit beta-1
G: Gamma-aminobutyric-acid receptor subunit beta-1
H: Gamma-aminobutyric-acid receptor subunit beta-1
I: Gamma-aminobutyric-acid receptor subunit beta-1
J: Gamma-aminobutyric-acid receptor subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)357,02220
Polymers353,83410
Non-polymers3,18910
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50910 Å2
ΔGint-296 kcal/mol
Surface area128340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.200, 266.650, 111.040
Angle α, β, γ (deg.)90.00, 107.71, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Gamma-aminobutyric-acid receptor subunit beta-1


Mass: 35383.367 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dickeya dadantii (strain 3937) (bacteria)
Strain: 3937 / Gene: Dda3937_00520 / Production host: Escherichia coli (E. coli) / References: UniProt: E0SJQ4
#2: Chemical
ChemComp-Z80 / 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine / Chlorpromazine


Mass: 318.864 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C17H19ClN2S / Comment: medication, antipsychotic*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.19 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium sulfate 50 mM ADA (N-(2-acetamido)iminodiacetic acid) pH 6.5 9-12 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.4→49.16 Å / Num. obs: 67372 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.8
Reflection shellRmerge(I) obs: 0.0371

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4a97

4a97


Resolution: 3.567→44.746 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 25.81
RfactorNum. reflection% reflection
Rfree0.2531 3412 5.06 %
Rwork0.22 --
obs0.2217 67372 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.567→44.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25045 0 210 0 25255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00525954
X-RAY DIFFRACTIONf_angle_d0.93335381
X-RAY DIFFRACTIONf_dihedral_angle_d16.14115083
X-RAY DIFFRACTIONf_chiral_restr0.0523899
X-RAY DIFFRACTIONf_plane_restr0.0054489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5674-3.61830.37441070.35311944X-RAY DIFFRACTION71
3.6183-3.67230.40341430.36192621X-RAY DIFFRACTION98
3.6723-3.72970.33741490.30982693X-RAY DIFFRACTION98
3.7297-3.79080.32431370.29232707X-RAY DIFFRACTION98
3.7908-3.85610.30451400.28332702X-RAY DIFFRACTION99
3.8561-3.92620.35391430.31082635X-RAY DIFFRACTION97
3.9262-4.00170.30461410.2592690X-RAY DIFFRACTION99
4.0017-4.08330.24481560.2362674X-RAY DIFFRACTION99
4.0833-4.1720.27281400.22332677X-RAY DIFFRACTION99
4.172-4.2690.25511290.21412742X-RAY DIFFRACTION99
4.269-4.37570.20481430.20332688X-RAY DIFFRACTION99
4.3757-4.49390.24051270.19222703X-RAY DIFFRACTION99
4.4939-4.6260.20721480.1782725X-RAY DIFFRACTION99
4.626-4.77510.19621310.16062695X-RAY DIFFRACTION99
4.7751-4.94560.18421430.17052685X-RAY DIFFRACTION99
4.9456-5.14330.20821470.16922708X-RAY DIFFRACTION99
5.1433-5.3770.20721640.17832671X-RAY DIFFRACTION99
5.377-5.660.22511520.18762708X-RAY DIFFRACTION99
5.66-6.01380.21711520.1982709X-RAY DIFFRACTION99
6.0138-6.47690.24611440.21082728X-RAY DIFFRACTION99
6.4769-7.12630.28451410.22522694X-RAY DIFFRACTION99
7.1263-8.15210.24951510.21092728X-RAY DIFFRACTION99
8.1521-10.25040.20481500.17742722X-RAY DIFFRACTION99
10.2504-44.7490.30161340.25632711X-RAY DIFFRACTION97

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more