[English] 日本語
Yorodumi
- EMDB-26845: EcMscK in an Open Conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26845
TitleEcMscK in an Open Conformation
Map dataEcMscK G924S mutant in an open conformation
Sample
  • Complex: E. coli MscK
    • Protein or peptide: Mechanosensitive channel MscK
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: 3.48 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 4, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26845.png

Downloads & links

-
Map

FileDownload / File: emd_26845.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEcMscK G924S mutant 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: 0.03
Minimum - Maximum-0.01760178 - 2.2333794
Average (Standard dev.)0.0015699867 (±0.022270598)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: Halfmap A

Fileemd_26845_half_map_1.map
AnnotationHalfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Halfmap B

Fileemd_26845_half_map_2.map
AnnotationHalfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : E. coli MscK

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

-
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

-
Macromolecule #1: Mechanosensitive channel MscK

MacromoleculeName: Mechanosensitive channel MscK / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K12
Molecular weightTheoretical: 127.378789 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MTMFQYYKRS RHFVFSAFIA FVFVLLCQNT AFARASSNGD LPTKADLQAQ LDSLNKQKDL SAQDKLVQQD LTDTLATLDK IDRIKEETV QLRQKVAEAP EKMRQATAAL TALSDVDNDE ETRKILSTLS LRQLETRVAQ ALDDLQNAQN DLASYNSQLV S LQTQPERV ...String:
MTMFQYYKRS RHFVFSAFIA FVFVLLCQNT AFARASSNGD LPTKADLQAQ LDSLNKQKDL SAQDKLVQQD LTDTLATLDK IDRIKEETV QLRQKVAEAP EKMRQATAAL TALSDVDNDE ETRKILSTLS LRQLETRVAQ ALDDLQNAQN DLASYNSQLV S LQTQPERV QNAMYNASQQ LQQIRSRLDG TDVGETALRP SQKVLMQAQQ ALLNAEIDQQ RKSLEGNTVL QDTLQKQRDY VT ANSARLE HQLQLLQEAV NSKRLTLTEK TAQEAVSPDE AARIQANPLV KQELEINQQL SQRLITATEN GNQLMQQNIK VKN WLERAL QSERNIKEQI AVLKGSLLLS RILYQQQQTL PSADELENMT NRIADLRLEQ FEVNQQRDAL FQSDAFVNKL EEGH TNEVN SEVHDALLQV VDMRRELLDQ LNKQLGNQLM MAINLQINQQ QLMSVSKNLK SILTQQIFWV NSNRPMDWDW IKAFP QSLK DEFKSMKITV NWQKAWPAVF IAFLAGLPLL LIAGLIHWRL GWLKAYQQKL ASAVGSLRND SQLNTPKAIL IDLIRA LPV CLIILAVGLI LLTMQLNISE LLWSFSKKLA IFWLVFGLCW KVLEKNGVAV RHFGMPEQQT SHWRRQIVRI SLALLPI HF WSVVAELSPL HLMDDVLGQA MIFFNLLLIA FLVWPMCRES WRDKESHTMR LVTITVLSII PIALMVLTAT GYFYTTLR L AGRWIETVYL VIIWNLLYQT VLRGLSVAAR RIAWRRALAR RQNLVKEGAE GAEPPEEPTI ALEQVNQQTL RITMLLMFA LFGVMFWAIW SDLITVFSYL DSITLWHYNG TEAGAAVVKN VTMGSLLFAI IASMVAWALI RNLPGLLEVL VLSRLNMRQG ASYAITTIL NYIIIAVGAM TVFGSLGVSW DKLQWLAAAL SVGLSFGLQE IFGNFVSGLI ILFERPVRIG DTVTIGSFSG T VSKIRIRA TTITDFDRKE VIIPNKAFVT ERLINWSLTD TTTRLVIRLG VAYGSDLEKV RKVLLKAATE HPRVMHEPMP EV FFTAFGA STLDHELRLY VRELRDRSRT VDELNRTIDQ LCRENDINIA FNQLEVHLHN EKGDEVTEVK RDYKGDDPTP AVG

UniProtKB: Mechanosensitive channel MscK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe specimen was homogeneous and monodisperse.

-
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

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.48 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)

-
Atomic model buiding 1

Initial modelPDB ID:

7uw5


Chain - Residue range: 496-1079 / Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: PHENIX
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7ux1:
EcMscK in an Open Conformation

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more