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- EMDB-24187: Structure of Mechanosensitive Ion Channel Flycatcher1 in GDN -

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Basic information

Entry
Database: EMDB / ID: EMD-24187
TitleStructure of Mechanosensitive Ion Channel Flycatcher1 in GDN
Map dataStructure of Mechanosensitive Ion Channel Flycatcher1 in GDN
Sample
  • Organelle or cellular component: FLYC1
    • Protein or peptide: Mechanosensitive ion channel Flycatcher1
  • Ligand: PALMITIC ACID
Keywordsmechanically activated ion channel / MEMBRANE PROTEIN
Biological speciesDionaea muscipula (Venus flytrap)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0882
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0882
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n5e
  • Surface level: 0.0882
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24187.png

Downloads & links

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Map

FileDownload / File: emd_24187.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Mechanosensitive Ion Channel Flycatcher1 in GDN
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 280 pix.
= 288.4 Å		1.03 Å/pix.
x 280 pix.
= 288.4 Å		1.03 Å/pix.
x 280 pix.
= 288.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0882 / Movie #1: 0.0882
Minimum - Maximum-0.0017463771 - 1.8514985
Average (Standard dev.)0.0013230073 (±0.025443325)
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-0.0021.8510.001

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Supplemental data

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Half map: Half map 1

Fileemd_24187_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_24187_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : FLYC1

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

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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

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Macromolecule #1: Mechanosensitive ion channel Flycatcher1

MacromoleculeName: Mechanosensitive ion channel Flycatcher1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / 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

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Macromolecule #2: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 2 / Number of copies: 7 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1100000
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 255359
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7n5e:
Structure of Mechanosensitive Ion Channel Flycatcher1 in GDN

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