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- EMDB-31197: Structure and Activity of SLAC1 Channels for Stomatal Signaling i... -

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Basic information

Entry
Database: EMDB / ID: EMD-31197
TitleStructure and Activity of SLAC1 Channels for Stomatal Signaling in Leaves
Map dataMap used for building. Post-processed from half maps using phenix.auto_sharpen.
Sample
  • Organelle or cellular component: Cryo-EM structure of Brachypodium distachyon SLAC1
Function / homology
Function and homology information


response to humidity / stomatal closure / regulation of stomatal opening / voltage-gated monoatomic anion channel activity / regulation of stomatal closure / response to ozone / intracellular monoatomic ion homeostasis / organic anion transport / response to abscisic acid / response to carbon dioxide ...response to humidity / stomatal closure / regulation of stomatal opening / voltage-gated monoatomic anion channel activity / regulation of stomatal closure / response to ozone / intracellular monoatomic ion homeostasis / organic anion transport / response to abscisic acid / response to carbon dioxide / multicellular organismal-level water homeostasis / response to light stimulus / protein phosphatase binding / membrane => GO:0016020 / protein kinase binding / plasma membrane
Similarity search - Function
S-type anion channel / Transporter protein SLAC1/Mae1/ Ssu1/TehA / Voltage-dependent anion channel superfamily / Voltage-dependent anion channel
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBrachypodium distachyon (stiff brome)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 2.97 Å
AuthorsDeng Y / Kashtoh H / Wang Q / Zhen GX / Li QY / Tang L / Gao HL / Zhang CR / Qin L / Su M ...Deng Y / Kashtoh H / Wang Q / Zhen GX / Li QY / Tang L / Gao HL / Zhang CR / Qin L / Su M / Li F / Huang XH / Wang YC / Xie Q / Clarke OB / Hendrickson WA / Chen YH
Funding support China, United States, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31470728 China
National Natural Science Foundation of China (NSFC)31322005 China
National Natural Science Foundation of China (NSFC)31872721 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107462 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM116799 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Structure and activity of SLAC1 channels for stomatal signaling in leaves.
Authors: Ya-Nan Deng / Hamdy Kashtoh / Quan Wang / Guang-Xiao Zhen / Qi-Yu Li / Ling-Hui Tang / Hai-Long Gao / Chun-Rui Zhang / Li Qin / Min Su / Fei Li / Xia-He Huang / Ying-Chun Wang / Qi Xie / ...Authors: Ya-Nan Deng / Hamdy Kashtoh / Quan Wang / Guang-Xiao Zhen / Qi-Yu Li / Ling-Hui Tang / Hai-Long Gao / Chun-Rui Zhang / Li Qin / Min Su / Fei Li / Xia-He Huang / Ying-Chun Wang / Qi Xie / Oliver B Clarke / Wayne A Hendrickson / Yu-Hang Chen /
Abstract: Stomata in leaves regulate gas exchange between the plant and its atmosphere. Various environmental stimuli elicit abscisic acid (ABA); ABA leads to phosphoactivation of slow anion channel 1 (SLAC1); ...Stomata in leaves regulate gas exchange between the plant and its atmosphere. Various environmental stimuli elicit abscisic acid (ABA); ABA leads to phosphoactivation of slow anion channel 1 (SLAC1); SLAC1 activity reduces turgor pressure in aperture-defining guard cells; and stomatal closure ensues. We used electrophysiology for functional characterizations of SLAC1 (SLAC1) and cryoelectron microscopy (cryo-EM) for structural analysis of SLAC1 (SLAC1), at 2.97-Å resolution. We identified 14 phosphorylation sites in SLAC1 and showed nearly 330-fold channel-activity enhancement with 4 to 6 of these phosphorylated. Seven SLAC1-conserved arginines are poised in SLAC1 for regulatory interaction with the N-terminal extension. This SLAC1 structure has its pores closed, in a basal state, spring loaded by phenylalanyl residues in high-energy conformations. SLAC1 phosphorylation fine-tunes an equilibrium between basal and activated SLAC1 trimers, thereby controlling the degree of stomatal opening.
History
DepositionApr 14, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.9
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 5.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7en0
  • Surface level: 5.9
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31197.png

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Map

FileDownload / File: emd_31197.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap used for building. Post-processed from half maps using phenix.auto_sharpen.
Voxel sizeX=Y=Z: 1.0475 Å
Density
Contour LevelBy AUTHOR: 5.9 / Movie #1: 5.9
Minimum - Maximum-21.821081 - 31.766413
Average (Standard dev.)-1.4013162e-11 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 209.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.04751.04751.0475
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z209.500209.500209.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-21.82131.766-0.000

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Supplemental data

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Mask #1

Fileemd_31197_msk_1.map
Projections & Slices
AxesZYX

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Half map: Half map B

Fileemd_31197_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: Half map A

Fileemd_31197_half_map_2.map
AnnotationHalf map A
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AxesZYX

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Sample components

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Entire : Cryo-EM structure of Brachypodium distachyon SLAC1

EntireName: Cryo-EM structure of Brachypodium distachyon SLAC1
Components
  • Organelle or cellular component: Cryo-EM structure of Brachypodium distachyon SLAC1

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Supramolecule #1: Cryo-EM structure of Brachypodium distachyon SLAC1

SupramoleculeName: Cryo-EM structure of Brachypodium distachyon SLAC1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Brachypodium distachyon (stiff brome)
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Acetate
GridModel: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 71.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.0.27) / Number images used: 95704
FSC plot (resolution estimation)

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