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- EMDB-6875: Structure of atOSCA3.1 channel -

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Basic information

Entry
Database: EMDB / ID: EMD-6875
TitleStructure of atOSCA3.1 channel
Map data
Sample
  • Complex: atOSCA3.1
    • Protein or peptide: CSC1-like protein ERD4
Keywordsosca / TMEM63 / ion channel / mechanosensitive / membrane protein / osmosensing / METAL TRANSPORT
Function / homology
Function and homology information


plasmodesma / plant-type vacuole / chloroplast envelope / calcium-activated cation channel activity / mRNA binding / nucleus / 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
CSC1-like protein ERD4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsChen L / Zhang M
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31622021 China
National Natural Science Foundation of China31521062 China
Ministry of Science and Technology of China2016YFA0502004 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
DepositionDec 26, 2017-
Header (metadata) releaseSep 12, 2018-
Map releaseSep 12, 2018-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-5z1f
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6875.png

Downloads & links

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Map

FileDownload / File: emd_6875.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 211. Å		1.06 Å/pix.
x 200 pix.
= 211. Å		1.06 Å/pix.
x 200 pix.
= 211. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.07859984 - 0.17347354
Average (Standard dev.)0.0019671735 (±0.009021612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 210.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0551.0551.055
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z211.000211.000211.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0790.1730.002

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Supplemental data

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Half map: #1

Fileemd_6875_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_6875_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : atOSCA3.1

EntireName: atOSCA3.1
Components
  • Complex: atOSCA3.1
    • Protein or peptide: CSC1-like protein ERD4

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Supramolecule #1: atOSCA3.1

SupramoleculeName: atOSCA3.1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 175 KDa

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Macromolecule #1: CSC1-like protein ERD4

MacromoleculeName: CSC1-like protein ERD4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 82.017727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEFGSFLVSL GTSFVIFVIL MLLFTWLSRK SGNAPIYYPN RILKGLEPWE GTSLTRNPFA WMREALTSSE QDVVNLSGVD TAVHFVFLS TVLGIFACSS LLLLPTLLPL AATDNNIKNT KNATDTTSKG TFSQLDNLSM ANITKKSSRL WAFLGAVYWI S LVTYFFLW ...String:
MEFGSFLVSL GTSFVIFVIL MLLFTWLSRK SGNAPIYYPN RILKGLEPWE GTSLTRNPFA WMREALTSSE QDVVNLSGVD TAVHFVFLS TVLGIFACSS LLLLPTLLPL AATDNNIKNT KNATDTTSKG TFSQLDNLSM ANITKKSSRL WAFLGAVYWI S LVTYFFLW KAYKHVSSLR AQALMSADVK PEQFAILVRD MPAPPDGQTQ KEFIDSYFRE IYPETFYRSL VATENSKVNK IW EKLEGYK KKLARAEAIL AATNNRPTNK TGFCGLVGKQ VDSIEYYTEL INESVAKLET EQKAVLAEKQ QTAAVVFFTT RVA AASAAQ SLHCQMVDKW TVTEAPEPRQ LLWQNLNIKL FSRIIRQYFI YFFVAVTILF YMIPIAFVSA ITTLKNLQRI IPFI KPVVE ITAIRTVLES FLPQIALIVF LAMLPKLLLF LSKAEGIPSQ SHAIRAASGK YFYFSVFNVF IGVTLAGTLF NTVKD IAKN PKLDMIINLL ATSLPKSATF FLTYVALKFF IGYGLELSRI IPLIIFHLKK KYLCKTEAEV KEAWYPGDLS YATRVP GDM LILTITFCYS VIAPLILIFG ITYFGLGWLV LRNQALKVYV PSYESYGRMW PHIHQRILAA LFLFQVVMFG YLGAKTF FY TALVIPLIIT SLIFGYVCRQ KFYGGFEHTA LEVACRELKQ SPDLEEIFRA YIPHSLSSHK PEEHEFKGAM SRYQDFNA I AGV

UniProtKB: CSC1-like protein ERD4

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
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: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 16322
Initial angle assignmentType: OTHER / Software - Name: RELION / Details: maximum likely hood in relion
Final angle assignmentType: OTHER / Software - Name: RELION
Details: stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms in cryosparc
Final 3D classificationNumber classes: 4
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-5z1f:
Structure of atOSCA3.1 channel

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