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Yorodumi- EMDB-3035: The structure of YnaI implies structural and mechanistic conserva... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3035 | |||||||||
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Title | The structure of YnaI implies structural and mechanistic conservation in the MscS-family of mechanosensitive channels | |||||||||
Map data | Reconstruction of YnaI | |||||||||
Sample |
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Keywords | YnaI / mechanosensitive channels / lipid-protein interaction / osmotic stress | |||||||||
Function / homology | Function and homology information mechanosensitive monoatomic ion channel activity / cellular response to osmotic stress / transmembrane transport / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.6 Å | |||||||||
Authors | Bottcher B / Prazak V / Rasmussen A / Black SS / Rasmussen T | |||||||||
Citation | Journal: Structure / Year: 2015 Title: The Structure of YnaI Implies Structural and Mechanistic Conservation in the MscS Family of Mechanosensitive Channels. Authors: Bettina Böttcher / Vojtech Prazak / Akiko Rasmussen / Susan S Black / Tim Rasmussen / Abstract: Mechanosensitive channels protect bacteria against lysis caused by a sudden drop in osmolarity in their surroundings. Besides the channel of large conductance (MscL) and small conductance (MscS), ...Mechanosensitive channels protect bacteria against lysis caused by a sudden drop in osmolarity in their surroundings. Besides the channel of large conductance (MscL) and small conductance (MscS), Escherichia coli has five additional paralogs of MscS that are functional and widespread in the bacterial kingdom. Here, we present the structure of YnaI by cryo-electron microscopy to a resolution of 13 Å. While the cytosolic vestibule is structurally similar to that in MscS, additional density is seen in the transmembrane (TM) region consistent with the presence of two additional TM helices predicted for YnaI. The location of this density suggests that the extra TM helices are tilted, which could induce local membrane curvature extending the tension-sensing paddles seen in MscS. Off-center lipid-accessible cavities are seen that resemble gaps between the sensor paddles in MscS. The conservation of the tapered shape and the cavities in YnaI suggest a mechanism similar to that of MscS. | |||||||||
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_3035.map.gz | 14.3 MB | EMDB map data format | |
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Header (meta data) | emd-3035-v30.xml emd-3035.xml | 20.8 KB 20.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3035_fsc.xml | 5.5 KB | Display | FSC data file |
Images | emd_3035.png | 99.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3035 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3035 | HTTPS FTP |
-Validation report
Summary document | emd_3035_validation.pdf.gz | 242.2 KB | Display | EMDB validaton report |
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Full document | emd_3035_full_validation.pdf.gz | 241.3 KB | Display | |
Data in XML | emd_3035_validation.xml.gz | 8.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3035 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3035 | HTTPS FTP |
-Related structure data
Similar structure data | |
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EM raw data | EMPIAR-10032 (Title: Cryo electron microscopy of YnaI / Data size: 107.6 Data #1: ynai_particles [picked particles - multiframe - processed] Data #2: ynai_micrographs [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_3035.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of YnaI | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.728 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Low conductance mechanosensitive channel YnaI
Entire | Name: Low conductance mechanosensitive channel YnaI |
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Components |
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-Supramolecule #1000: Low conductance mechanosensitive channel YnaI
Supramolecule | Name: Low conductance mechanosensitive channel YnaI / type: sample / ID: 1000 / Oligomeric state: 7 / Number unique components: 1 |
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Molecular weight | Theoretical: 271 KDa |
-Macromolecule #1: YnaI
Macromolecule | Name: YnaI / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Oligomeric state: heptamer / Recombinant expression: No |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: MJF641 / Location in cell: Pasma membrane |
Molecular weight | Theoretical: 38.76 KDa |
Sequence | UniProtKB: Low conductance mechanosensitive channel YnaI / GO: transmembrane transport InterPro: Mechanosensitive ion channel MscS, Mechanosensitive ion channel MscS, transmembrane-2, LSM domain superfamily, Mechanosensitive ion channel MscS, C-terminal, Mechanosensitive ion channel MscS, conserved site |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.2 mg/mL |
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Buffer | pH: 7.2 |
Grid | Details: 1.2/1.3 Quantifoil 400 mesh copper Rh/grids, glow discharge for 1 min in air |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: HOMEMADE PLUNGER Method: blot for 15 s with 2 layers of filter paper Whatman No 1 before plunging into Ethane cooled by N2; heater is used for preventing freezing of ethane; plunger has an environmental chamber, ...Method: blot for 15 s with 2 layers of filter paper Whatman No 1 before plunging into Ethane cooled by N2; heater is used for preventing freezing of ethane; plunger has an environmental chamber, which is humidified with 2 water soaked sponges (Bellare Design); Bellare design of |
-Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TECNAI F20 |
Temperature | Average: 95 K |
Alignment procedure | Legacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing |
Date | Mar 15, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Electron microscopy #2
Microscopy ID | 2 |
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Microscope | FEI TECNAI F20 |
Temperature | Average: 95 K |
Alignment procedure | Legacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing |
Date | Mar 15, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Electron microscopy #3
Microscopy ID | 3 |
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Microscope | FEI TECNAI F20 |
Temperature | Average: 95 K |
Alignment procedure | Legacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing |
Date | Apr 7, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Electron microscopy #4
Microscopy ID | 4 |
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Microscope | FEI TECNAI F20 |
Temperature | Average: 95 K |
Alignment procedure | Legacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing |
Date | Apr 15, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Electron microscopy #5
Microscopy ID | 5 |
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Microscope | FEI TECNAI F20 |
Temperature | Average: 95 K |
Alignment procedure | Legacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing |
Date | Apr 17, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Electron microscopy #6
Microscopy ID | 6 |
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Microscope | FEI TECNAI F20 |
Temperature | Average: 95 K |
Alignment procedure | Legacy - Astigmatism: at 200,000 magnification on carbon; computationally during image processing |
Date | Apr 19, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Digitization - Sampling interval: 15.6 µm / Number real images: 3308 / Average electron dose: 25 e/Å2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 5.7 µm / Nominal defocus min: 1.39 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G |
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Software | Name: Chimera |
Details | The structure of the related MscS (2oAU) was fitted manually as rigid body, the fit was optimized by the fit in map option of chimera using residues 129-281 of MscS (cytosolic part) |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: overlap |