+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26854 | |||||||||
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Title | EcMscK in an intermediate conformation | |||||||||
Map data | EcMscK in an intermediate conformation | |||||||||
Sample |
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Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.97 Å | |||||||||
Authors | Mount JW / Yuan P | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for mechanotransduction in a potassium-dependent mechanosensitive ion channel. Authors: Jonathan Mount / Grigory Maksaev / Brock T Summers / James A J Fitzpatrick / Peng Yuan / Abstract: Mechanosensitive channels of small conductance, found in many living organisms, open under elevated membrane tension and thus play crucial roles in biological response to mechanical stress. Amongst ...Mechanosensitive channels of small conductance, found in many living organisms, open under elevated membrane tension and thus play crucial roles in biological response to mechanical stress. Amongst these channels, MscK is unique in that its activation also requires external potassium ions. To better understand this dual gating mechanism by force and ligand, we elucidate distinct structures of MscK along the gating cycle using cryo-electron microscopy. The heptameric channel comprises three layers: a cytoplasmic domain, a periplasmic gating ring, and a markedly curved transmembrane domain that flattens and expands upon channel opening, which is accompanied by dilation of the periplasmic ring. Furthermore, our results support a potentially unifying mechanotransduction mechanism in ion channels depicted as flattening and expansion of the transmembrane domain. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26854.map.gz | 198.2 MB | EMDB map data format | |
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Header (meta data) | emd-26854-v30.xml emd-26854.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26854_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_26854.png | 166.4 KB | ||
Others | emd_26854_half_map_1.map.gz emd_26854_half_map_2.map.gz | 225.3 MB 225.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26854 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26854 | HTTPS FTP |
-Validation report
Summary document | emd_26854_validation.pdf.gz | 580.3 KB | Display | EMDB validaton report |
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Full document | emd_26854_full_validation.pdf.gz | 579.9 KB | Display | |
Data in XML | emd_26854_validation.xml.gz | 22 KB | Display | |
Data in CIF | emd_26854_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26854 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26854 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26854.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | EcMscK in an intermediate conformation | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half A
File | emd_26854_half_map_1.map | ||||||||||||
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Annotation | Half A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half B
File | emd_26854_half_map_2.map | ||||||||||||
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Annotation | Half B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : EcMscK in an intermediate conformation
Entire | Name: EcMscK in an intermediate conformation |
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Components |
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-Supramolecule #1: EcMscK in an intermediate conformation
Supramolecule | Name: EcMscK in an intermediate conformation / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Homomeric Heptamer |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
-Macromolecule #1: EcMscK
Macromolecule | Name: EcMscK / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MTMFQYYKRS RHFVFSAFIA FVFVLLCQNT AFARASSNGD LPTKADLQAQ LDSLNKQKDL SAQDKLVQQ DLTDTLATLD KIDRIKEETV QLRQKVAEAP EKMRQATAAL TALSDVDNDE E TRKILSTL SLRQLETRVA QALDDLQNAQ NDLASYNSQL VSLQTQPERV ...String: MTMFQYYKRS RHFVFSAFIA FVFVLLCQNT AFARASSNGD LPTKADLQAQ LDSLNKQKDL SAQDKLVQQ DLTDTLATLD KIDRIKEETV QLRQKVAEAP EKMRQATAAL TALSDVDNDE E TRKILSTL SLRQLETRVA QALDDLQNAQ NDLASYNSQL VSLQTQPERV QNAMYNASQQ LQ QIRSRLD GTDVGETALR PSQKVLMQAQ QALLNAEIDQ QRKSLEGNTV LQDTLQKQRD YVT ANSARL EHQLQLLQEA VNSKRLTLTE KTAQEAVSPD EAARIQANPL VKQELEINQQ LSQR LITAT ENGNQLMQQN IKVKNWLERA LQSERNIKEQ IAVLKGSLLL SRILYQQQQT LPSAD ELEN MTNRIADLRL EQFEVNQQRD ALFQSDAFVN KLEEGHTNEV NSEVHDALLQ VVDMRR ELL DQLNKQLGNQ LMMAINLQIN QQQLMSVSKN LKSILTQQIF WVNSNRPMDW DWIKAFP QS LKDEFKSMKI TVNWQKAWPA VFIAFLAGLP LLLIAGLIHW RLGWLKAYQQ KLASAVGS L RNDSQLNTPK AILIDLIRAL PVCLIILAVG LILLTMQLNI SELLWSFSKK LAIFWLVFG LCWKVLEKNG VAVRHFGMPE QQTSHWRRQI VRISLALLPI HFWSVVAELS PLHLMDDVLG QAMIFFNLL LIAFLVWPMC RESWRDKESH TMRLVTITVL SIIPIALMVL TATGYFYTTL R LAGRWIET VYLVIIWNLL YQTVLRGLSV AARRIAWRRA LARRQNLVKE GAEGAEPPEE PT IALEQVN QQTLRITMLL MFALFGVMFW AIWSDLITVF SYLDSITLWH YNGTEAGAAV VKN VTMGSL LFAIIASMVA WALIRNLPGL LEVLVLSRLN MRQGASYAIT TILNYIIIAV GAMT VFGSL GVSWDKLQWL AAALSVGLSF GLQEIFGNFV SGLIILFERP VRIGDTVTIG SFSGT VSKI RIRATTITDF DRKEVIIPNK AFVTERLINW SLTDTTTRLV IRLGVAYGSD LEKVRK VLL KAATEHPRVM HEPMPEVFFT AFGASTLDHE LRLYVRELRD RSRTVDELNR TIDQLCR EN DINIAFNQLE VHLHNEKGDE VTEVKRDYKG DDPTPAVG |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7 mg/mL | |||||||||||||||
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Buffer | pH: 8 Component:
Details: Micrographs were pooled from protein purified in the presence of either 150 mM NaCl or 150 mM KCl. Buffers were prepared fresh, degassed, and filtered through a 0.45 um Durapore PVDF membrane. | |||||||||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | The sample was homogeneous and monodisperse. |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 46.16 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 150000 |
Sample stage | Cooling holder cryogen: NITROGEN |