[English] 日本語
Yorodumi
- EMDB-76007: Core of EcMscM in NaCl in a closed conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-76007
TitleCore of EcMscM in NaCl in a closed conformation
Map dataEMReady sharpened map
Sample
  • Complex: MscM
    • Protein or peptide: Miniconductance mechanosensitive channel MscM
KeywordsMechanosensitive / Ion channel / MscS / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / cellular response to osmotic stress / 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
Similarity search - Domain/homology
Miniconductance mechanosensitive channel MscM
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHiotis G / Walz T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01 GM144581 United States
CitationJournal: Nat Commun / Year: 2026
Title: The bacterial mechanosensitive channel MscM gates through concerted changes in its transmembrane and cytoplasmic domains.
Authors: Giorgos Hiotis / Thomas Walz /
Abstract: The mechanosensitive channel of small conductance (MscS) is the founding member of the family of MscS-like channels, which share a structurally conserved core but feature additional structural ...The mechanosensitive channel of small conductance (MscS) is the founding member of the family of MscS-like channels, which share a structurally conserved core but feature additional structural elements that define their specific channel characteristics. Here, we characterize the structure and function of the Escherichia coli mechanosensitive channel of mini conductance (MscM), which features eight additional transmembrane (TM) helices and a large periplasmic domain. Our cryo-EM structures reveal that channel gating involves conformational changes in all domains of MscM. In particular, a cytoplasmic extension of TM7 couples the conformation of the TM domain to that of the cytoplasmic domain, resulting in gating of its lateral fenestrations, where ions enter the channel. Thus, different from all other MscS-like channels studied to date, channel gating in MscM is mediated by its cytoplasmic domain and not the TM domain, which senses changes in membrane tension and operates the cytoplasmic gates.
History
DepositionMar 11, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_76007.png

Downloads & links

-
Map

FileDownload / File: emd_76007.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMReady sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 450 pix.
= 381.15 Å		0.85 Å/pix.
x 450 pix.
= 381.15 Å		0.85 Å/pix.
x 450 pix.
= 381.15 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.847 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-0.20770665 - 18.018234
Average (Standard dev.)0.011677279 (±0.28243554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 381.15 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened map

Fileemd_76007_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_76007_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_76007_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MscM

EntireName: MscM
Components
  • Complex: MscM
    • Protein or peptide: Miniconductance mechanosensitive channel MscM

-
Supramolecule #1: MscM

SupramoleculeName: MscM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Macromolecule #1: Miniconductance mechanosensitive channel MscM

MacromoleculeName: Miniconductance mechanosensitive channel MscM / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 124.824023 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MRLIITFLMA WCLSWGAYAA TAPDSKQITQ ELEQAKAAKP AQPEVVEALQ SALNALEERK GSLERIKQYQ QVIDNYPKLS ATLRAQLNN MRDEPRSVSP GMSTDALNQE ILQVSSQLLD KSRQAQQEQE RAREIADSLN QLPQQQTDAR RQLNEIERRL G TLTGNTPL ...String:
MRLIITFLMA WCLSWGAYAA TAPDSKQITQ ELEQAKAAKP AQPEVVEALQ SALNALEERK GSLERIKQYQ QVIDNYPKLS ATLRAQLNN MRDEPRSVSP GMSTDALNQE ILQVSSQLLD KSRQAQQEQE RAREIADSLN QLPQQQTDAR RQLNEIERRL G TLTGNTPL NQAQNFALQS DSARLKALVD ELELAQLSAN NRQELARLRS ELAEKESQQL DAYLQALRNQ LNSQRQLEAE RA LESTELL AENSADLPKD IVAQFKINRE LSAALNQQAQ RMDLVASQQR QAASQTLQVR QALNTLREQS QWLGSSNLLG EAL RAQVAR LPEMPKPQQL DTEMAQLRVQ RLRYEDLLNK QPLLRQIHQA DGQPLTAEQN RILEAQLRTQ RELLNSLLQG GDTL LLELT KLKVSNGQLE DALKEVNEAT HRYLFWTSDV RPMTIAWPLE IAQDLRRLIS LDTFSQLGKA SVMMLTSKET ILPLF GALI LVGCSIYSRR YFTRFLERSA AKVGKVTQDH FWLTLRTLFW SILVASPLPV LWMTLGYGLR EAWPYPLAVA IGDGVT ATV PLLWVVMICA TFARPNGLFI AHFGWPRERV SRGMRYYLMS IGLIVPLIMA LMMFDNLDDR EFSGSLGRLC FILICGA LA VVTLSLKKAG IPLYLNKEGS GDNITNHMLW NMMIGAPLVA ILASAVGYLA TAQALLARLE TSVAIWFLLL VVYHVIRR W MLIQRRRLAF DRAKHRRAEM LAQRARGEEE AHHHSSPEGA IEVDESEVDL DAISAQSLRL VRSILMLIAL LSVIVLWSE IHSAFGFLEN ISLWDVTSTV QGVESLEPIT LGAVLIAILV FIITTQLVRN LPALLELAIL QHLDLTPGTG YAITTITKYL LMLIGGLVG FSMIGIEWSK LQWLVAALGV GLGFGLQEIF ANFISGLIIL FEKPIRIGDT VTIRDLTGSV TKINTRATTI S DWDRKEII VPNKAFITEQ FINWSLSDSV TRVVLTIPAP ADANSEEVTE ILLTAARRCS LVIDNPAPEV FLVDLQQGIQ IF ELRIYAA EMGHRMPLRH EIHQLILAGF HAHGIDMPFP PFQMRLESLN GKQTGRTLTS AGKGRQAGSL LEVLFQ

UniProtKB: Miniconductance mechanosensitive channel MscM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
30.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
0.02 mg/mlGDNGlyco-diosgenin
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.2 sec. / Average electron dose: 46.21 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio reconstruction
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50627
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX
Output model

PDB-11sm:
Core of EcMscM in NaCl in a closed 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