[English] 日本語
Yorodumi
- EMDB-41043: Structure of mechanically activated ion channel OSCA1.2 in peptidiscs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41043
TitleStructure of mechanically activated ion channel OSCA1.2 in peptidiscs
Map dataOSCA1.2 in peptidisc postprocessed with LocalDeblur
Sample
  • Complex: OSCA1.2 in peptidisc
    • Complex: OSCA1.2
      • Protein or peptide: Calcium permeable stress-gated cation channel 1
    • Complex: peptidisc peptide
      • Protein or peptide: NSPr peptide
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: PALMITIC ACID
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: CHOLESTEROL
Keywordsmechanically activated ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


mechanosensitive monoatomic ion channel activity / calcium-activated cation channel activity / monoatomic cation transport / identical protein binding / plasma membrane
Similarity search - Function
CSC1/OSCA1-like, 7TM region / CSC1/OSCA1-like, cytosolic domain / CSC1/OSCA1-like, N-terminal transmembrane domain / Calcium permeable stress-gated cation channel 1-like / Calcium-dependent channel, 7TM region, putative phosphate / Late exocytosis, associated with Golgi transport / Cytosolic domain of 10TM putative phosphate transporter
Similarity search - Domain/homology
Calcium permeable stress-gated cation channel 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBurendei B / Jojoa-Cruz S / Lee WH / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL143297 United States
CitationJournal: Structure / Year: 2024
Title: Structure of mechanically activated ion channel OSCA2.3 reveals mobile elements in the transmembrane domain.
Authors: Sebastian Jojoa-Cruz / Batuujin Burendei / Wen-Hsin Lee / Andrew B Ward /
Abstract: Members of the OSCA/TMEM63 family are mechanically activated ion channels and structures of some OSCA members have revealed the architecture of these channels and structural features that are ...Members of the OSCA/TMEM63 family are mechanically activated ion channels and structures of some OSCA members have revealed the architecture of these channels and structural features that are potentially involved in mechanosensation. However, these structures are all in a similar state and information about the motion of different elements of the structure is limited, preventing a deeper understanding of how these channels work. Here, we used cryoelectron microscopy to determine high-resolution structures of Arabidopsis thaliana OSCA1.2 and OSCA2.3 in peptidiscs. The structure of OSCA1.2 matches previous structures of the same protein in different environments. Yet, in OSCA2.3, the TM6a-TM7 linker adopts a different conformation that constricts the pore on its cytoplasmic side. Furthermore, coevolutionary sequence analysis uncovered a conserved interaction between the TM6a-TM7 linker and the beam-like domain (BLD). Our results reveal conformational heterogeneity and differences in conserved interactions between the TMD and BLD among members of the OSCA family.
History
DepositionJun 12, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41043.png

Downloads & links

-
Map

FileDownload / File: emd_41043.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOSCA1.2 in peptidisc postprocessed with LocalDeblur
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 220 pix.
= 226.6 Å		1.03 Å/pix.
x 220 pix.
= 226.6 Å		1.03 Å/pix.
x 220 pix.
= 226.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0138
Minimum - Maximum-0.0027878035 - 0.08646044
Average (Standard dev.)0.000037965154 (±0.00249654)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 226.59999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: OSCA1.2 in peptidisc postprocessed with DeepEMhancer "highRes" model

Fileemd_41043_additional_1.map
AnnotationOSCA1.2 in peptidisc postprocessed with DeepEMhancer "highRes" model
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: OSCA1.2 in peptidisc half map 2

Fileemd_41043_half_map_1.map
AnnotationOSCA1.2 in peptidisc half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: OSCA1.2 in peptidisc half map 1

Fileemd_41043_half_map_2.map
AnnotationOSCA1.2 in peptidisc half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : OSCA1.2 in peptidisc

EntireName: OSCA1.2 in peptidisc
Components
  • Complex: OSCA1.2 in peptidisc
    • Complex: OSCA1.2
      • Protein or peptide: Calcium permeable stress-gated cation channel 1
    • Complex: peptidisc peptide
      • Protein or peptide: NSPr peptide
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: PALMITIC ACID
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: CHOLESTEROL

-
Supramolecule #1: OSCA1.2 in peptidisc

SupramoleculeName: OSCA1.2 in peptidisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 176 KDa

-
Supramolecule #2: OSCA1.2

SupramoleculeName: OSCA1.2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Supramolecule #3: peptidisc peptide

SupramoleculeName: peptidisc peptide / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes

-
Macromolecule #1: Calcium permeable stress-gated cation channel 1

MacromoleculeName: Calcium permeable stress-gated cation channel 1 / type: protein_or_peptide / ID: 1
Details: The last 10 residues (GTGTLEVLFQ) are leftover of a linker and protease site.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 89.031719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATLQDIGVS AGINILSAFV FFIIFAVLRL QPFNDRVYFS KWYLKGLRSS PARGGAFAQR FVNLDFRSYM KFLNWMPEAL KMPEPELID HAGLDSVVYL RIYWLGLKIF TPIAVLAWAV LVPVNWTNNT LEMAKQLRNV TSSDIDKLSV SNIPEYSMRF W THIVMAYA ...String:
MATLQDIGVS AGINILSAFV FFIIFAVLRL QPFNDRVYFS KWYLKGLRSS PARGGAFAQR FVNLDFRSYM KFLNWMPEAL KMPEPELID HAGLDSVVYL RIYWLGLKIF TPIAVLAWAV LVPVNWTNNT LEMAKQLRNV TSSDIDKLSV SNIPEYSMRF W THIVMAYA FTIWTCYVLM KEYETIANMR LQFVASEARR PDQFTVLVRN VPPDADESVS ELVEHFFLVN HPDHYLTHQV VC NANKLAD LVKKKKKLQN WLDYYQLKYA RNNSQRIMVK LGFLGLWGQK VDAIEHYIAE IDKISKEISK EREEVVNDPK AIM PAAFVS FKTRWAAAVC AQTQQTRNPT QWLTEWAPEP RDVFWSNLAI PYVSLTVRRL IMHVAFFFLT FFFIVPIAFV QSLA TIEGI VKAAPFLKFI VDDKFMKSVI QGFLPGIALK LFLAFLPSIL MIMSKFEGFT SISSLERRAA FRYYIFNLVN VFLAS VIAG AAFEQLNSFL NQSANQIPKT IGVAIPMKAT FFITYIMVDG WAGVAGEILM LKPLIMFHLK NAFLVKTDKD REEAMD PGS IGFNTGEPRI QLYFLLGLVY APVTPMLLPF ILVFFALAYI VYRHQIINVY NQEYESAAAF WPDVHGRVIA ALVISQL LL MGLLGTKHAA LAAPFLIALP VLTIGFHHFC KGRYEPAFIR YPLQEAMMKD TLETAREPNL NLKGYLQNAY VHPVFKGD E DDYDIDDKLG KFEDEAIIVP TKRQSRRNTP APSIISGDDS PSLPFSGKLV GTGTLEVLFQ

UniProtKB: Calcium permeable stress-gated cation channel 1

-
Macromolecule #2: NSPr peptide

MacromoleculeName: NSPr peptide / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.482132 KDa
SequenceString:
FAEKFKEAVK DYFAKFWDPA AEKLKEAVKD YFAKLWD

-
Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 26 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

-
Macromolecule #5: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 5 / Number of copies: 2 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

-
Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 6 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMsodium chlorideNaCl
2.0 mMdithiothreitol
GridMaterial: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 1 / Number real images: 1805 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1046049
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Details: SIDESPLITTER was used for reconstruction step / Number images used: 52250
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6mgv


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8t56:
Structure of mechanically activated ion channel OSCA1.2 in peptidiscs

+
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