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- EMDB-24186: Composite Structure of Mechanosensitive Ion Channel Flycatcher1 in GDN -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-24186 | |||||||||||||||
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Title | Composite Structure of Mechanosensitive Ion Channel Flycatcher1 in GDN | |||||||||||||||
![]() | Composite Structure of Mechanosensitive Ion Channel Flycatcher1 in GDN | |||||||||||||||
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![]() | mechanically activated ion channel / MEMBRANE PROTEIN | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||
![]() | Jojoa-Cruz S / Saotome K / Lee WH / Patapoutian A / Ward AB | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
Images | ![]() | 114.6 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7n5dMC ![]() 7n5eC ![]() 7n5fC ![]() 7n5gC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | |
EM raw data | ![]() Data size: 5.7 TB Data #1: Unaligned multi-frame micrographs of FLYC1 in GDN, dataset 1 [micrographs - multiframe] Data #2: Unaligned multi-frame micrographs of FLYC1 in GDN, dataset 2 [micrographs - multiframe] Data #3: Gain references for dataset 1 and dataset 2 [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite Structure of Mechanosensitive Ion Channel Flycatcher1 in GDN | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : FLYC1
Entire | Name: FLYC1 |
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Components |
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-Supramolecule #1: FLYC1
Supramolecule | Name: FLYC1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 607 KDa |
-Macromolecule #1: Mechanosensitive ion channel Flycatcher1
Macromolecule | Name: Mechanosensitive ion channel Flycatcher1 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 86.814523 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 2 / Number of copies: 7 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 7 mg/mL | ||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7n5d: |