[English] 日本語
Yorodumi
- EMDB-51489: Sub-open structure of the mechanosensitive channel YbiO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51489
TitleSub-open structure of the mechanosensitive channel YbiO
Map data
Sample
  • Complex: MscS-like core of YbiO in GDN/CHS detergent
    • Protein or peptide: Mechanosensitive channel protein
KeywordsMechanosensitive / MscS-like / YbiO / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / plasma membrane
Similarity search - Function
Mechanosensitive ion channel YbiO / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / 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
Mechanosensitive channel protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsLane BJ / Pliotas C
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S018069/1 United Kingdom
Wellcome Trust219999/Z/19/Z United Kingdom
CitationJournal: TO BE PUBLISHED
Title: Sub-open structure of the mechanosensitive channel YbiO
Authors: Lane BJ / Pliotas C
History
DepositionSep 4, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51489.png

Downloads & links

-
Map

FileDownload / File: emd_51489.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 576 pix.
= 426.24 Å		0.74 Å/pix.
x 576 pix.
= 426.24 Å		0.74 Å/pix.
x 576 pix.
= 426.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.1621696 - 0.760477
Average (Standard dev.)0.0023861746 (±0.03301004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 426.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_51489_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51489_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51489_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : MscS-like core of YbiO in GDN/CHS detergent

EntireName: MscS-like core of YbiO in GDN/CHS detergent
Components
  • Complex: MscS-like core of YbiO in GDN/CHS detergent
    • Protein or peptide: Mechanosensitive channel protein

-
Supramolecule #1: MscS-like core of YbiO in GDN/CHS detergent

SupramoleculeName: MscS-like core of YbiO in GDN/CHS detergent / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: Mechanosensitive channel protein

MacromoleculeName: Mechanosensitive channel protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 83.047555 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRWILFILFC LLGAPAHAVS IPGVTTTTTT DSTTEPAPEP DIEQKKAAYG ALADVLDNDT SRKELIDQLR TVAATPPAEP VPKIVPPTL VEEQTVLQKV TEVSRHYGEA LSARFGQLYR NITGSPHKPF NPQTFSNALT HFSMLAVLVF GFYWLIRLCA L PLYRKMGQ ...String:
MRWILFILFC LLGAPAHAVS IPGVTTTTTT DSTTEPAPEP DIEQKKAAYG ALADVLDNDT SRKELIDQLR TVAATPPAEP VPKIVPPTL VEEQTVLQKV TEVSRHYGEA LSARFGQLYR NITGSPHKPF NPQTFSNALT HFSMLAVLVF GFYWLIRLCA L PLYRKMGQ WARQKNRERS NWLQLPAMII GAFIIDLLLL ALTLFVGQVL SDNLNAGSRT IAFQQSLFLN AFALIEFFKA VL RLIFCPN VAELRPFTIQ DESARYWSRR LSWLSSLIGY GLIVAVPIIS NQVNVQIGAL ANVIIMLCMT VWALYLIFRN KKE ITQHLL NFAEHSLAFF SLFIRAFALV WHWLASAYFI VLFFFSLFDP GNSLKFMMGA TVRSLAIIGI AAFVSGMFSR WLAK TITLS PHTQRNYPEL QKRLNGWLSA ALKTARILTV CVAVMLLLSA WGLFDFWNWL QNGAGQKTVD ILIRIALILF FSAVG WTVL ASLIENRLAS DIHGRPLPSA RTRTLLTLFR NALAVIISTI TIMIVLSEIG VNIAPLLAGA GALGLAISFG SQTLVK DII TGVFIQFENG MNTGDLVTIG PLTGTVERMS IRSVGVRQDT GAYHIIPWSS ITTFANFVRG IGSVVANYDV DRHEDAD KA NQALKDAVAE LMENEEIRGL IIGEPNFAGI VGLSNTAFTL RVSFTTLPLK QWTVRFALDS QVKKHFDLAG VRAPVQTY Q VLPAPGATPA EPLPPGEPTL LEHHHHHH

UniProtKB: Mechanosensitive channel protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.1 mg/mL
BufferpH: 7.4
GridMaterial: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Average electron dose: 66.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 147935
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 4 / Avg.num./class: 131625 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

+
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