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- EMDB-32633: Cryo-EM structure of AtSLAC1 S59A mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-32633
TitleCryo-EM structure of AtSLAC1 S59A mutant
Map dataCryo-EM map of the AtSLAC1 S59A mutant
Sample
  • Complex: Trimeric structure of the anion channel SLAC1
    • Protein or peptide: Guard cell S-type anion channel SLAC1
Function / homology
Function and homology information


response to humidity / stomatal closure / regulation of stomatal opening / inorganic anion transport / voltage-gated monoatomic anion channel activity / regulation of stomatal closure / stomatal movement / response to ozone / intracellular monoatomic ion homeostasis / organic anion transport ...response to humidity / stomatal closure / regulation of stomatal opening / inorganic anion transport / voltage-gated monoatomic anion channel activity / regulation of stomatal closure / stomatal movement / response to ozone / intracellular monoatomic ion homeostasis / organic anion transport / monoatomic anion transmembrane transporter activity / response to abscisic acid / response to carbon dioxide / multicellular organismal-level water homeostasis / monoatomic anion transport / abscisic acid-activated signaling pathway / response to light stimulus / protein phosphatase binding / protein kinase binding / membrane / 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
Guard cell S-type anion channel SLAC1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSun L / Liu X / Li Y
Funding support China, 6 items
OrganizationGrant numberCountry
Other governmentXDB37020103 China
National Natural Science Foundation of China (NSFC)31900885 China
National Natural Science Foundation of China (NSFC)31870732 China
Other government2008085MC90 China
Other government2008085J15 China
Other governmentYD9100002004 China
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the Arabidopsis guard cell anion channel SLAC1 suggests activation mechanism by phosphorylation.
Authors: Yawen Li / Yinan Ding / Lili Qu / Xinru Li / Qinxuan Lai / Pingxia Zhao / Yongxiang Gao / Chengbin Xiang / Chunlei Cang / Xin Liu / Linfeng Sun /
Abstract: Stomata play a critical role in the regulation of gas exchange and photosynthesis in plants. Stomatal closure participates in multiple stress responses, and is regulated by a complex network ...Stomata play a critical role in the regulation of gas exchange and photosynthesis in plants. Stomatal closure participates in multiple stress responses, and is regulated by a complex network including abscisic acid (ABA) signaling and ion-flux-induced turgor changes. The slow-type anion channel SLAC1 has been identified to be a central controller of stomatal closure and phosphoactivated by several kinases. Here, we report the structure of SLAC1 in Arabidopsis thaliana (AtSLAC1) in an inactivated, closed state. The cytosolic amino (N)-terminus and carboxyl (C)-terminus of AtSLAC1 are partially resolved and form a plug-like structure which packs against the transmembrane domain (TMD). Breaking the interactions between the cytosolic plug and transmembrane domain triggers channel activation. An inhibition-release model is proposed for SLAC1 activation by phosphorylation that the cytosolic plug dissociates from the transmembrane domain upon phosphorylation, and induces conformational changes to open the pore. These findings facilitate our understanding of the regulation of SLAC1 activity and stomatal aperture in plants.
History
DepositionJan 19, 2022-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateOct 26, 2022-
Current statusOct 26, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32633.png

Downloads & links

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Map

FileDownload / File: emd_32633.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of the AtSLAC1 S59A mutant
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-4.7176204 - 7.6844964
Average (Standard dev.)0.005069456 (±0.17208464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 2

Fileemd_32633_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_32633_half_map_2.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric structure of the anion channel SLAC1

EntireName: Trimeric structure of the anion channel SLAC1
Components
  • Complex: Trimeric structure of the anion channel SLAC1
    • Protein or peptide: Guard cell S-type anion channel SLAC1

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Supramolecule #1: Trimeric structure of the anion channel SLAC1

SupramoleculeName: Trimeric structure of the anion channel SLAC1 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F

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Macromolecule #1: Guard cell S-type anion channel SLAC1

MacromoleculeName: Guard cell S-type anion channel SLAC1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 63.311742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MERKQSNAHS TFADINEVED EAEQELQQQE NNNNKRFSGN RGPNRGKQRP FRGFSRQVSL ETGFSVLNRE SRERDDKKSL PRSGRSFGG FESGGIINGG DGRKTDFSMF RTKSTLSKQK SLLPSIIRER DIENSLRTED GETKDDSINE NVSAGRYFAA L RGPELDEV ...String:
MERKQSNAHS TFADINEVED EAEQELQQQE NNNNKRFSGN RGPNRGKQRP FRGFSRQVSL ETGFSVLNRE SRERDDKKSL PRSGRSFGG FESGGIINGG DGRKTDFSMF RTKSTLSKQK SLLPSIIRER DIENSLRTED GETKDDSINE NVSAGRYFAA L RGPELDEV KDNEDILLPK EEQWPFLLRF PIGCFGICLG LSSQAVLWLA LAKSPATNFL HITPLINLVV WLFSLVVLVS VS FTYILKC IFYFEAVKRE YFHPVRVNFF FAPWVVCMFL AISVPPMFSP NRKYLHPAIW CVFMGPYFFL ELKIYGQWLS GGK RRLCKV ANPSSHLSVV GNFVGAILAS KVGWDEVAKF LWAVGFAHYL VVFVTLYQRL PTSEALPKEL HPVYSMFIAA PSAA SIAWN TIYGQFDGCS RTCFFIALFL YISLVARINF FTGFKFSVAW WSYTFPMTTA SVATIKYAEA VPGYPSRALA LTLSF ISTA MVCVLFVSTL LHAFVWQTLF PNDLAIAITK RKLTREKKPF KRAYDLKRWT KQALAKKISA EKDFEAEEES HH

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.0 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 264751
FSC plot (resolution estimation)

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