[English] 日本語
Yorodumi
- EMDB-19937: 6-channel super-structure of the Mechanosensitive Ion Channel of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19937
Title6-channel super-structure of the Mechanosensitive Ion Channel of Small Conductance 2 from Nematocida displodere
Map dataSix homo-heptameric channels, formed by Nematocida displodere Mechanosensitive ion channel of small conductance 2, form a higher oligomeric structure resembling a six-way cross joint.
Sample
  • Complex: Six homo-heptameric mechanosensitive ion channel of small conductance 2
    • Organelle or cellular component: Homo-heptameric mechanosensitive ion channel of small conductance 2
KeywordsMembrane protein / channel protein
Biological speciesNematocida displodere (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.3 Å
AuthorsBerg A / Barandun J / Berntsson RP-A
Funding support Sweden, European Union, 4 items
OrganizationGrant numberCountry
Swedish Research Council2016-03599 Sweden
Swedish Research Council2023-02423 Sweden
Swedish Research Council2019-02011 Sweden
European Research Council (ERC)PolTube 948655European Union
CitationJournal: To Be Published
Title: Nematocida displodere Mechanosensitive Ion Channel of Small Conductance 2 assembles into a unique 6-channel super-structure in vitro
Authors: Berg A / Barandun J / Berntsson RP-A
History
DepositionMar 25, 2024-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19937.png

Downloads & links

-
Map

FileDownload / File: emd_19937.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSix homo-heptameric channels, formed by Nematocida displodere Mechanosensitive ion channel of small conductance 2, form a higher oligomeric structure resembling a six-way cross joint.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 384 pix.
= 307.2 Å		0.8 Å/pix.
x 384 pix.
= 307.2 Å		0.8 Å/pix.
x 384 pix.
= 307.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0043
Minimum - Maximum-0.006190855 - 0.022504931
Average (Standard dev.)-0.000017393802 (±0.0008858824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 307.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19937_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_19937_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19937_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19937_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Six homo-heptameric mechanosensitive ion channel of small conduct...

EntireName: Six homo-heptameric mechanosensitive ion channel of small conductance 2
Components
  • Complex: Six homo-heptameric mechanosensitive ion channel of small conductance 2
    • Organelle or cellular component: Homo-heptameric mechanosensitive ion channel of small conductance 2

-
Supramolecule #1: Six homo-heptameric mechanosensitive ion channel of small conduct...

SupramoleculeName: Six homo-heptameric mechanosensitive ion channel of small conductance 2
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Nematocida displodere (fungus)
Molecular weightTheoretical: 64 KDa

-
Supramolecule #2: Homo-heptameric mechanosensitive ion channel of small conductance 2

SupramoleculeName: Homo-heptameric mechanosensitive ion channel of small conductance 2
type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Nematocida displodere (fungus)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.288 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMHEPES-KOH
300.0 mMSodium chlorideNaCl
0.05 %DDM
1.0 mMDTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 2000 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 190000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 13 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Software - details: beta / Number images used: 157712
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationNumber classes: 4 / Avg.num./class: 88000 / Software - Name: RELION (ver. 5.0) / Software - details: beta
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://pdbjlvh1.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