+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11560 | |||||||||
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Title | YnaI in an open-like conformation | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information mechanosensitive monoatomic ion channel activity / cellular response to osmotic stress / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Flegler VJ / Rasmussen A / Rao S / Wu N / Zenobi R / Sansom MSP / Hedrich R / Rasmussen T / Boettcher B | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: The MscS-like channel YnaI has a gating mechanism based on flexible pore helices. Authors: Vanessa Judith Flegler / Akiko Rasmussen / Shanlin Rao / Na Wu / Renato Zenobi / Mark S P Sansom / Rainer Hedrich / Tim Rasmussen / Bettina Böttcher / Abstract: The mechanosensitive channel of small conductance (MscS) is the prototype of an evolutionarily diversified large family that fine-tunes osmoregulation but is likely to fulfill additional functions. ...The mechanosensitive channel of small conductance (MscS) is the prototype of an evolutionarily diversified large family that fine-tunes osmoregulation but is likely to fulfill additional functions. has six osmoprotective paralogs with different numbers of transmembrane helices. These helices are important for gating and sensing in MscS but the role of the additional helices in the paralogs is not understood. The medium-sized channel YnaI was extracted and delivered in native nanodiscs in closed-like and open-like conformations using the copolymer diisobutylene/maleic acid (DIBMA) for structural studies. Here we show by electron cryomicroscopy that YnaI has an extended sensor paddle that during gating relocates relative to the pore concomitant with bending of a GGxGG motif in the pore helices. YnaI is the only one of the six paralogs that has this GGxGG motif allowing the sensor paddle to move outward. Access to the pore is through a vestibule on the cytosolic side that is fenestrated by side portals. In YnaI, these portals are obstructed by aromatic side chains but are still fully hydrated and thus support conductance. For comparison with large-sized channels, we determined the structure of YbiO, which showed larger portals and a wider pore with no GGxGG motif. Further in silico comparison of MscS, YnaI, and YbiO highlighted differences in the hydrophobicity and wettability of their pores and vestibule interiors. Thus, MscS-like channels of different sizes have a common core architecture but show different gating mechanisms and fine-tuned conductive properties. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11560.map.gz | 28.4 MB | EMDB map data format | |
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Header (meta data) | emd-11560-v30.xml emd-11560.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11560_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_11560.png | 46.2 KB | ||
Masks | emd_11560_msk_1.map | 30.5 MB | Mask map | |
Others | emd_11560_additional_1.map.gz emd_11560_half_map_1.map.gz emd_11560_half_map_2.map.gz | 28.1 MB 28.2 MB 28.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11560 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11560 | HTTPS FTP |
-Related structure data
Related structure data | 6zyeMC 6zydC 7a46C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11560.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0635 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11560_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_11560_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_11560_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11560_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : open-like YnaI in DIBMA treated with LPC
Entire | Name: open-like YnaI in DIBMA treated with LPC |
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Components |
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-Supramolecule #1: open-like YnaI in DIBMA treated with LPC
Supramolecule | Name: open-like YnaI in DIBMA treated with LPC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: YnaI was purified with the detergent DDM and reconstituted into liposomes. After addition of LPC it was extracted using DIBMA co-polymer. |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 278 KDa |
-Macromolecule #1: YnaI,Low conductance mechanosensitive channel YnaI
Macromolecule | Name: YnaI,Low conductance mechanosensitive channel YnaI / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 42.927254 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)MI ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)MI AELFTNNALN LVIIFGSCAA LILMSFWFRR GNRKRKGFLF HAVQFLIYTI IISAVGSI I NYVIENYKLK FITPGVIDFI CTSLIAVILT IKLFLLINQF EKQQIKKGRD ITSARIMSRI IKITIIVVLV LLYGEHFGM SLSGLLTFGG IGGLAVGMAG KDILSNFFSG IMLYFDRPFS IGDWIRSPDR NIEGTVAEIG WRITKITTFD NRPLYVPNSL FSSISVENP GRMTNRRITT TIGLRYEDAA KVGVIVEAVR EMLKNHPAID QRQTLLVYFN QFADSSLNIM VYCFTKTTVW A EWLAAQQD VYLKIIDIVQ SHGADFAFPS QTLYMDNITP PEQGRLEHHH HHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 4161 / Average exposure time: 63.0 sec. / Average electron dose: 70.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |