[English] 日本語
Yorodumi
- EMDB-20986: Unliganded ELIC in POPC-only nanodiscs. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20986
TitleUnliganded ELIC in POPC-only nanodiscs.
Map dataUnliganded ELIC in POPC-only nanodiscs
Sample
  • Complex: Unliganded ELIC in POPC-only nanodiscs.
    • Protein or peptide: Gamma-aminobutyric-acid receptor subunit beta-1
KeywordsPentameric Ligand-gated Ion Channels / POPC / Nanodisc / Cys-loop receptors / MEMBRANE PROTEIN
Function / homology
Function and homology information


extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / membrane / identical protein binding
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-aminobutyric-acid receptor subunit beta-1
Similarity search - Component
Biological speciesDickeya dadantii 3937 (bacteria) / Dickeya dadantii (strain 3937) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsGrosman C / Kumar P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS042169 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer.
Authors: Pramod Kumar / Yuhang Wang / Zhening Zhang / Zhiyu Zhao / Gisela D Cymes / Emad Tajkhorshid / Claudio Grosman /
Abstract: The lipid dependence of the nicotinic acetylcholine receptor from the electric organ has long been recognized, and one of the most consistent experimental observations is that, when reconstituted in ...The lipid dependence of the nicotinic acetylcholine receptor from the electric organ has long been recognized, and one of the most consistent experimental observations is that, when reconstituted in membranes formed by zwitterionic phospholipids alone, exposure to agonist fails to elicit ion-flux activity. More recently, it has been suggested that the bacterial homolog ELIC ( ligand-gated ion channel) has a similar lipid sensitivity. As a first step toward the elucidation of the structural basis of this phenomenon, we solved the structures of ELIC embedded in palmitoyl-oleoyl-phosphatidylcholine- (POPC-) only nanodiscs in both the unliganded (4.1-Å resolution) and agonist-bound (3.3 Å) states using single-particle cryoelectron microscopy. Comparison of the two structural models revealed that the largest differences occur at the level of loop C-at the agonist-binding sites-and the loops at the interface between the extracellular and transmembrane domains (ECD and TMD, respectively). On the other hand, the transmembrane pore is occluded in a remarkably similar manner in both structures. A straightforward interpretation of these findings is that POPC-only membranes frustrate the ECD-TMD coupling in such a way that the "conformational wave" of liganded-receptor gating takes place in the ECD and the interfacial M2-M3 linker but fails to penetrate the membrane and propagate into the TMD. Furthermore, analysis of the structural models and molecular simulations suggested that the higher affinity for agonists characteristic of the open- and desensitized-channel conformations results, at least in part, from the tighter confinement of the ligand to its binding site; this limits the ligand's fluctuations, and thus delays its escape into bulk solvent.
History
DepositionNov 18, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseJan 15, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6v0b
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20986.png

Downloads & links

-
Map

FileDownload / File: emd_20986.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnliganded ELIC in POPC-only nanodiscs
Voxel sizeX=Y=Z: 1.0961 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.05
Minimum - Maximum-0.109495215 - 0.20002368
Average (Standard dev.)0.0012950337 (±0.0086040115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 219.22 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09611.09611.0961
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z219.220219.220219.220
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1090.2000.001

-
Supplemental data

-
Half map: Unliganded ELIC in POPC-only nanodiscs.

Fileemd_20986_half_map_1.map
AnnotationUnliganded ELIC in POPC-only nanodiscs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unliganded ELIC in POPC-only nanodiscs

Fileemd_20986_half_map_2.map
AnnotationUnliganded ELIC in POPC-only nanodiscs
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Unliganded ELIC in POPC-only nanodiscs.

EntireName: Unliganded ELIC in POPC-only nanodiscs.
Components
  • Complex: Unliganded ELIC in POPC-only nanodiscs.
    • Protein or peptide: Gamma-aminobutyric-acid receptor subunit beta-1

-
Supramolecule #1: Unliganded ELIC in POPC-only nanodiscs.

SupramoleculeName: Unliganded ELIC in POPC-only nanodiscs. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Dickeya dadantii 3937 (bacteria)

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

MacromoleculeName: Gamma-aminobutyric-acid receptor subunit beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Dickeya dadantii (strain 3937) (bacteria) / Strain: 3937
Molecular weightTheoretical: 36.879 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: APADNAADAR PVDVSVSIFI NKIYGVNTLE QTYKVDGYIV AQWTGKPRKT PGDKPLIVEN TQIERWINNG LWVPALEFIN VVGSPDTGN KRLMLFPDGR VIYNARFLGS FSNDMDFRLF PFDRQQFVLE LEPFSYNNQQ LRFSDIQVYT ENIDNEEIDE W WIRGKAST ...String:
APADNAADAR PVDVSVSIFI NKIYGVNTLE QTYKVDGYIV AQWTGKPRKT PGDKPLIVEN TQIERWINNG LWVPALEFIN VVGSPDTGN KRLMLFPDGR VIYNARFLGS FSNDMDFRLF PFDRQQFVLE LEPFSYNNQQ LRFSDIQVYT ENIDNEEIDE W WIRGKAST HISDIRYDHL SSVQPNQNEF SRITVRIDAV RNPSYYLWSF ILPLGLIIAA SWSVFWLESF SERLQTSFTL ML TVVAYAF YTSNILPRLP YTTVIDQMII AGYGSIFAAI LLIIFAHHRQ ANGVEDDLLI QRCRLAFPLG FLAIGCVLVI RGI TL

UniProtKB: Gamma-aminobutyric-acid receptor subunit beta-1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
10.0 mMNa2HPO4Sodium phospate buffer
NaH2PO4Sodium phospate buffer
150.0 mMNaClSodium chlorideSodium Chloride

Details: 150 mM NaCl and 10 mM sodium phosphate, pH 8.0.
GridModel: Homemade / Material: GOLD
VitrificationCryogen name: ETHANE / Instrument: SPOTITON

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Detector mode: COUNTING / Average electron dose: 63.56 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 289375
Startup modelType of model: PDB ENTRY
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 29207

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6v0b:
Unliganded ELIC in POPC-only nanodiscs.

+
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