[English] 日本語
Yorodumi
- EMDB-6822: Structure of atOSCA1.1 channel -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6822
TitleStructure of atOSCA1.1 channel
Map datasharpened, used for model building
Sample
  • Complex: atOSCA1.1
    • Protein or peptide: Protein OSCA1
Function / homology
Function and homology information


regulation of calcium ion import / cellular hyperosmotic response / calcium-activated cation channel activity / response to osmotic stress / monoatomic cation channel activity / protein tetramerization / plasma membrane / cytosol
Similarity search - Function
Calcium permeable stress-gated cation channel 1-like / CSC1/OSCA1-like, 7TM region / CSC1/OSCA1-like, cytosolic domain / CSC1/OSCA1-like, N-terminal transmembrane domain / Calcium-dependent channel, 7TM region, putative phosphate / Late exocytosis, associated with Golgi transport / Cytosolic domain of 10TM putative phosphate transporter
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsChen L / Zhang M / Kang Y / Wu JX
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31622021 China
Ministry of Science and Technology (China)2016YFA0502004 China
National Natural Science Foundation of China31521062 China
CitationJournal: Nat Struct Mol Biol / Year: 2018
Title: Structure of the mechanosensitive OSCA channels.
Authors: Mingfeng Zhang / Dali Wang / Yunlu Kang / Jing-Xiang Wu / Fuqiang Yao / Chengfang Pan / Zhiqiang Yan / Chen Song / Lei Chen /
Abstract: Mechanosensitive ion channels convert mechanical stimuli into a flow of ions. These channels are widely distributed from bacteria to higher plants and humans, and are involved in many crucial ...Mechanosensitive ion channels convert mechanical stimuli into a flow of ions. These channels are widely distributed from bacteria to higher plants and humans, and are involved in many crucial physiological processes. Here we show that two members of the OSCA protein family in Arabidopsis thaliana, namely AtOSCA1.1 and AtOSCA3.1, belong to a new class of mechanosensitive ion channels. We solve the structure of the AtOSCA1.1 channel at 3.5-Å resolution and AtOSCA3.1 at 4.8-Å resolution by cryo-electron microscopy. OSCA channels are symmetric dimers that are mediated by cytosolic inter-subunit interactions. Strikingly, they have structural similarity to the mammalian TMEM16 family proteins. Our structural analysis accompanied with electrophysiological studies identifies the ion permeation pathway within each subunit and suggests a conformational change model for activation.
History
DepositionSep 10, 2017-
Header (metadata) releaseSep 12, 2018-
Map releaseSep 12, 2018-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6jpf
  • Surface level: 0.45
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6822.png

Downloads & links

-
Map

FileDownload / File: emd_6822.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened, used for model building
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.45
Minimum - Maximum-1.2517332 - 2.0028458
Average (Standard dev.)0.0032147025 (±0.07109888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z256.000256.000256.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.2522.0030.003

-
Supplemental data

-
Mask #1

Fileemd_6822_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_6822_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_6822_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : atOSCA1.1

EntireName: atOSCA1.1
Components
  • Complex: atOSCA1.1
    • Protein or peptide: Protein OSCA1

-
Supramolecule #1: atOSCA1.1

SupramoleculeName: atOSCA1.1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 175 KDa

-
Macromolecule #1: Protein OSCA1

MacromoleculeName: Protein OSCA1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 87.697008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATLKDIGVS AGINILTAFI FFIIFAFLRL QPFNDRVYFS KWYLRGLRSS PASGGGFAGR FVNLELRSYL KFLHWMPEAL KMPERELID HAGLDSVVYL RIYWLGLKIF APIAMLAWAV LVPVNWTNNE LELAKHFKNV TSSDIDKLTI SNIPEGSNRF W AHIIMAYA ...String:
MATLKDIGVS AGINILTAFI FFIIFAFLRL QPFNDRVYFS KWYLRGLRSS PASGGGFAGR FVNLELRSYL KFLHWMPEAL KMPERELID HAGLDSVVYL RIYWLGLKIF APIAMLAWAV LVPVNWTNNE LELAKHFKNV TSSDIDKLTI SNIPEGSNRF W AHIIMAYA FTIWTCYMLM KEYETVANMR LQFLASEGRR PDQFTVLVRN VPPDPDETVS ELVEHFFLVN HPDNYLTHQV VC NANKLAD LVSKKTKLQN WLDYYQLKYT RNNSQIRPIT KLGCLGLCGQ KVDAIEHYIA EVDKTSKEIA EERENVVNDQ KSV MPASFV SFKTRWAAAV CAQTTQTRNP TEWLTEWAAE PRDIYWPNLA IPYVSLTVRR LVMNVAFFFL TFFFIIPIAF VQSL ATIEG IEKVAPFLKV IIEKDFIKSL IQGLLAGIAL KLFLIFLPAI LMTMSKFEGF TSVSFLERRS ASRYYIFNLV NVFLG SVIA GAAFEQLNSF LNQSPNQIPK TIGMAIPMKA TFFITYIMVD GWAGVAGEIL MLKPLIIYHL KNAFLVKTEK DREEAM NPG SIGFNTGEPQ IQLYFLLGLV YAPVTPMLLP FILVFFALAY VVYRHQIINV YNQEYESAAA FWPDVHGRVI TALIISQ LL LMGLLGTKHA ASAAPFLIAL PVITIGFHRF CKGRFEPAFV RYPLQEAMMK DTLERAREPN LNLKGYLQDA YIHPVFKG G DNDDDGDMIG KLENEVIIVP TKRQSRRNTP APSRISGESS PSLAVINGKE V

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER
Details: stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms in cryosparc
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Details: stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms in cryosparc
Final 3D classificationNumber classes: 4
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
Details: stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms in cryosparc
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 115697

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6jpf:
Structure of atOSCA1.1 channel at 3.52A

+
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