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- EMDB-26877: Locally refined core of EcMscK in an open conformation -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-26877
TitleLocally refined core of EcMscK in an open conformation
Map dataLocally refined core of EcMscK G924S in an open conformation.
Sample
  • Complex: E. coli MscK
    • Protein or peptide: EcMscK
Keywordsmembrane protein / mechanosensation / ion channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


intracellular water homeostasis / response to potassium ion / mechanosensitive monoatomic ion channel activity / potassium ion transport / plasma membrane
Similarity search - Function
Mechanosensitive ion channel MscS, porin domain / Mechanosensitive ion channel inner membrane domain 1 / : / Mechanosensitive ion channel inner membrane domain 1 / Mechanosensitive ion channel porin domain / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site ...Mechanosensitive ion channel MscS, porin domain / Mechanosensitive ion channel inner membrane domain 1 / : / Mechanosensitive ion channel inner membrane domain 1 / Mechanosensitive ion channel porin domain / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / LSM domain superfamily / P-type ATPase, transmembrane domain superfamily
Similarity search - Domain/homology
Mechanosensitive channel MscK
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 Å
AuthorsMount JW / Yuan P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS099341 United States
CitationJournal: 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
DepositionMay 8, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26877.png

Downloads & links

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Map

FileDownload / File: emd_26877.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally refined core of EcMscK G924S in an open conformation.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 400 pix.
= 376. Å		0.94 Å/pix.
x 400 pix.
= 376. Å		0.94 Å/pix.
x 400 pix.
= 376. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.04943219 - 1.9736235
Average (Standard dev.)0.0007122204 (±0.016850065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 376.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half A

Fileemd_26877_half_map_1.map
AnnotationHalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half B

Fileemd_26877_half_map_2.map
AnnotationHalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli MscK

EntireName: E. coli MscK
Components
  • Complex: E. coli MscK
    • Protein or peptide: EcMscK

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Supramolecule #1: E. coli MscK

SupramoleculeName: E. coli MscK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Homomeric Heptamer
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Location in cell: Inner Membrane

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Macromolecule #1: EcMscK

MacromoleculeName: EcMscK / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: 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

UniProtKB: Mechanosensitive channel MscK

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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:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
150.0 mMKClPotassium Chloride
20.0 mMTris-HCl
0.02 %Glyco-Diosgenin

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.
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe specimen was homogeneous and monodisperse.

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Average electron dose: 46.16 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 94414
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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