[English] 日本語
Yorodumi
- EMDB-20862: Extended Sensor Paddles with Bound Lipids Revealed in Mechanosens... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20862
TitleExtended Sensor Paddles with Bound Lipids Revealed in Mechanosensitive Channel YnaI
Map dataStructure of a mechanosensitive channel
Sample
  • Complex: YnaI with PS lipids
    • Protein or peptide: Low conductance mechanosensitive channel YnaI
  • Ligand: O-{(R)-hydroxy[(2R)-3-(icosyloxy)-2-(tetradecanoyloxy)propoxy]phosphoryl}-L-serine
Keywordsmechanosensitive channel / Phosphoserine lipid / complete paddle / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / cellular response to osmotic stress / identical protein binding / plasma membrane
Similarity search - Function
Mechanosensitive ion channel protein YnaI-like / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS ...Mechanosensitive ion channel protein YnaI-like / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / LSM domain superfamily
Similarity search - Domain/homology
Low conductance mechanosensitive channel YnaI
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsHu W / Wang Z
CitationJournal: Commun Biol / Year: 2021
Title: Mechanosensitive channel YnaI has lipid-bound extended sensor paddles.
Authors: Wenxin Hu / Zhiming Wang / Hongjin Zheng /
Abstract: The general mechanism of bacterial mechanosensitive channels (MS) has been characterized by extensive studies on a small conductance channel MscS from Escherichia coli (E. coli). However, recent ...The general mechanism of bacterial mechanosensitive channels (MS) has been characterized by extensive studies on a small conductance channel MscS from Escherichia coli (E. coli). However, recent structural studies on the same channel have revealed controversial roles of various channel-bound lipids in channel gating. To better understand bacterial MscS-like channels, it is necessary to characterize homologs other than MscS. Here, we describe the structure of YnaI, one of the closest MscS homologs in E. coli, in its non-conducting state at 3.3 Å resolution determined by cryo electron microscopy. Our structure revealed the intact membrane sensor paddle domain in YnaI, which was stabilized by functionally important residues H43, Q46, Y50 and K93. In the pockets between sensor paddles, there were clear lipid densities that interact strongly with residues Q100 and R120. These lipids were a mixture of natural lipids but may be enriched in cardiolipin and phosphatidylserine. In addition, residues along the ion-conducting pathway and responsible for the heptameric assembly were discussed. Together with biochemical experiments and mutagenesis studies, our results provide strong support for the idea that the pocket lipids are functionally important for mechanosensitive channels.
History
DepositionOct 24, 2019-
Header (metadata) releaseNov 20, 2019-
Map releaseOct 28, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6urt
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20862.png

Downloads & links

-
Map

FileDownload / File: emd_20862.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of a mechanosensitive channel
Voxel sizeX=Y=Z: 0.864 Å
Density
Contour LevelBy AUTHOR: 0.0064 / Movie #1: 0.007
Minimum - Maximum-0.009268312 - 0.035084482
Average (Standard dev.)0.000016125712 (±0.0012478394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 304.12802 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8640.8640.864
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z304.128304.128304.128
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.0090.0350.000

-
Supplemental data

-
Sample components

-
Entire : YnaI with PS lipids

EntireName: YnaI with PS lipids
Components
  • Complex: YnaI with PS lipids
    • Protein or peptide: Low conductance mechanosensitive channel YnaI
  • Ligand: O-{(R)-hydroxy[(2R)-3-(icosyloxy)-2-(tetradecanoyloxy)propoxy]phosphoryl}-L-serine

-
Supramolecule #1: YnaI with PS lipids

SupramoleculeName: YnaI with PS lipids / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 270 KDa

-
Macromolecule #1: Low conductance mechanosensitive channel YnaI

MacromoleculeName: Low conductance mechanosensitive channel YnaI / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 38.792344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIAELFTNNA LNLVIIFGSC AALILMSFWF RRGNRKRKGF LFHAVQFLIY TIIISAVGSI INYVIENYKL KFITPGVIDF ICTSLIAVI LTIKLFLLIN QFEKQQIKKG RDITSARIMS RIIKITIIVV LVLLYGEHFG MSLSGLLTFG GIGGLAVGMA G KDILSNFF ...String:
MIAELFTNNA LNLVIIFGSC AALILMSFWF RRGNRKRKGF LFHAVQFLIY TIIISAVGSI INYVIENYKL KFITPGVIDF ICTSLIAVI LTIKLFLLIN QFEKQQIKKG RDITSARIMS RIIKITIIVV LVLLYGEHFG MSLSGLLTFG GIGGLAVGMA G KDILSNFF SGIMLYFDRP FSIGDWIRSP DRNIEGTVAE IGWRITKITT FDNRPLYVPN SLFSSISVEN PGRMTNRRIT TT IGLRYED AAKVGVIVEA VREMLKNHPA IDQRQTLLVY FNQFADSSLN IMVYCFTKTT VWAEWLAAQQ DVYLKIIDIV QSH GADFAF PSQTLYMDNI TPPEQGR

UniProtKB: Low conductance mechanosensitive channel YnaI

-
Macromolecule #2: O-{(R)-hydroxy[(2R)-3-(icosyloxy)-2-(tetradecanoyloxy)propoxy]pho...

MacromoleculeName: O-{(R)-hydroxy[(2R)-3-(icosyloxy)-2-(tetradecanoyloxy)propoxy]phosphoryl}-L-serine
type: ligand / ID: 2 / Number of copies: 7 / Formula: QGD
Molecular weightTheoretical: 750.038 Da
Chemical component information

ChemComp-QGD:
O-{(R)-hydroxy[(2R)-3-(icosyloxy)-2-(tetradecanoyloxy)propoxy]phosphoryl}-L-serine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5 mg/mL
BufferpH: 7.5
Details: 20mM HEPES pH7.5, 150mM NaCl, 0.01% LMNG, 3mM Fluorinated Fos-Cholin 8
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 64.3 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178000
FSC plot (resolution estimation)

+
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