[English] 日本語
Yorodumi
- EMDB-24188: Structure of Mechanosensitive Ion Channel Flycatcher1 Protomer in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-24188
TitleStructure of Mechanosensitive Ion Channel Flycatcher1 Protomer in 'Down' conformation in GDN
Map dataFocused map of 'Down' protomer of Mechanosensitive Ion Channel Flycatcher1 in GDN
Sample
  • Organelle or cellular component: FLYC1
    • Protein or peptide: Mechanosensitive ion channel Flycatcher1
  • Ligand: PALMITIC ACID
Biological speciesDionaea muscipula (Venus flytrap)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsJojoa-Cruz S / Saotome K / Lee WH / Patapoutian A / Ward AB
Funding support United States, United Kingdom, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL143297 United States
Wellcome Trust208361/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N000145/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/R004722/1 United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into the Venus flytrap mechanosensitive ion channel Flycatcher1.
Authors: Sebastian Jojoa-Cruz / Kei Saotome / Che Chun Alex Tsui / Wen-Hsin Lee / Mark S P Sansom / Swetha E Murthy / Ardem Patapoutian / Andrew B Ward /
Abstract: Flycatcher1 (FLYC1), a MscS homolog, has recently been identified as a candidate mechanosensitive (MS) ion channel involved in Venus flytrap prey recognition. FLYC1 is a larger protein and its ...Flycatcher1 (FLYC1), a MscS homolog, has recently been identified as a candidate mechanosensitive (MS) ion channel involved in Venus flytrap prey recognition. FLYC1 is a larger protein and its sequence diverges from previously studied MscS homologs, suggesting it has unique structural features that contribute to its function. Here, we characterize FLYC1 by cryo-electron microscopy, molecular dynamics simulations, and electrophysiology. Akin to bacterial MscS and plant MSL1 channels, we find that FLYC1 central core includes side portals in the cytoplasmic cage that regulate ion preference and conduction, by identifying critical residues that modulate channel conductance. Topologically unique cytoplasmic flanking regions can adopt 'up' or 'down' conformations, making the channel asymmetric. Disruption of an up conformation-specific interaction severely delays channel deactivation by 40-fold likely due to stabilization of the channel open state. Our results illustrate novel structural features and likely conformational transitions that regulate mechano-gating of FLYC1.
History
DepositionJun 5, 2021-
Header (metadata) releaseFeb 16, 2022-
Map releaseFeb 16, 2022-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.088
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.088
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7n5f
  • Surface level: 0.088
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7n5f
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24188.png

Downloads & links

-
Map

FileDownload / File: emd_24188.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map of 'Down' protomer of Mechanosensitive Ion Channel Flycatcher1 in GDN
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.0882 / Movie #1: 0.088
Minimum - Maximum-0.0017395475 - 1.7858655
Average (Standard dev.)0.0014839643 (±0.027461449)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 288.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z288.400288.400288.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0021.7860.001

-
Supplemental data

-
Half map: Half-map 2

Fileemd_24188_half_map_1.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 1

Fileemd_24188_half_map_2.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FLYC1

EntireName: FLYC1
Components
  • Organelle or cellular component: FLYC1
    • Protein or peptide: Mechanosensitive ion channel Flycatcher1
  • Ligand: PALMITIC ACID

-
Supramolecule #1: FLYC1

SupramoleculeName: FLYC1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Dionaea muscipula (Venus flytrap) / Organ: Trap / Tissue: Trigger hair
Molecular weightTheoretical: 607 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pEG

-
Macromolecule #1: Mechanosensitive ion channel Flycatcher1

MacromoleculeName: Mechanosensitive ion channel Flycatcher1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dionaea muscipula (Venus flytrap) / Organ: Trap / Tissue: Trigger hair
Molecular weightTheoretical: 86.814523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSYLHEPPG DEPSMRIEQP KTADRAPEQV AIHICEPSKV VTESFPFSET AEPEAKSKNC PCPEIARIGP CPNKPPKIPI NRGLSRIST NKSRPKSRFG EPSWPVESSL DLTSQSPVSP YREEAFSVEN CGTAGSRRGS FARGTTSRAA SSSRKDETKE G PDEKEVYQ ...String:
MGSYLHEPPG DEPSMRIEQP KTADRAPEQV AIHICEPSKV VTESFPFSET AEPEAKSKNC PCPEIARIGP CPNKPPKIPI NRGLSRIST NKSRPKSRFG EPSWPVESSL DLTSQSPVSP YREEAFSVEN CGTAGSRRGS FARGTTSRAA SSSRKDETKE G PDEKEVYQ RVTAQLSARN QKRMTVKLMI ELSVFLCLLG CLVCSLTVDG FKRYTVIGLD IWKWFLLLLV IFSGMLITHW IV HVAVFFV EWKFLMRKNV LYFTHGLKTS VEVFIWITVV LATWVMLIKP DVNQPHQTRK ILEFVTWTIV TVLIGAFLWL VKT TLLKIL ASSFHLNRFF DRIQESVFHH SVLQTLAGRP VVELAQGISR TESQDGAGQV SFMEHTKTQN KKVVDVGKLH QMKQ EKVPA WTMQLLVDVV SNSGLSTMSG MLDEDMVEGG VELDDDEITN EEQAIATAVR IFDNIVQDKV DQSYIDRVDL HRFLI WEEV DHLFPLFEVN EKGQISLKAF AKWVVKVYND QAALKHALND NKTAVKQLNK LVTAILIVMM IVIWLIVTGI ATTKLI VLL SSQLVVAAFI FGNTCKTIFE AIIFVFVMHP FDVGDRCVID GNKMLVEEMN ILTTVFLKWD KEKVYYPNSI LCTKAIG NF FRSPDQGDVL EFSVDFTTPV LKIGDLKDRI KMYLEQNLNF WHPQHNMVVK EIENVNKIKM ALFVNHTINF QDFAEKNR R RSELVLELKK IFEELDIKYN LLPQEISIRN MGSGSLEVLF Q

-
Macromolecule #2: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration7 mg/mL
BufferpH: 8
Component:
ConcentrationName
25.0 mMHEPES
150.0 mMNaClSodium chloride
0.0004 mg/mLleupeptin
0.0004 mg/mLaprotinin
0.0004 mMpepstatin
0.2 mMphenylmethylsulfonyl fluoridePMSF
0.4 mMdiothiothreitol
0.04 %GDN
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1100000
CTF correctionSoftware:
Namedetails
Gctf (ver. 1.06)For CryoSPARC
CTFFIND (ver. 4)For RELION
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Details: Symmetry expanded particles / Number images used: 145362
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7n5f:
Structure of Mechanosensitive Ion Channel Flycatcher1 Protomer in 'Down' conformation in GDN

+
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