+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34303 | |||||||||||||||
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Title | AtSLAC1 6D mutant in closed state | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Stomatal closure / anion channel / phosphorylation-dependent activation / MEMBRANE PROTEIN | |||||||||||||||
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 / response to carbon dioxide / monoatomic anion transmembrane transporter activity / response to abscisic acid / multicellular organismal-level water homeostasis / monoatomic anion transport / abscisic acid-activated signaling pathway / response to light stimulus / bioluminescence / generation of precursor metabolites and energy / protein phosphatase binding / protein kinase binding / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Lee Y / Lee S | |||||||||||||||
Funding support | Korea, Republic Of, 4 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM structures of the plant anion channel SLAC1 from Arabidopsis thaliana suggest a combined activation model. Authors: Yeongmok Lee / Hyeon Seong Jeong / Seoyeon Jung / Junmo Hwang / Chi Truc Han Le / Sung-Hoon Jun / Eun Jo Du / KyeongJin Kang / Beom-Gi Kim / Hyun-Ho Lim / Sangho Lee / Abstract: The anion channel SLAC1 functions as a crucial effector in the ABA signaling, leading to stomata closure. SLAC1 is activated by phosphorylation in its intracellular domains. Both a binding-activation ...The anion channel SLAC1 functions as a crucial effector in the ABA signaling, leading to stomata closure. SLAC1 is activated by phosphorylation in its intracellular domains. Both a binding-activation model and an inhibition-release model for activation have been proposed based on only the closed structures of SLAC1, rendering the structure-based activation mechanism controversial. Here we report cryo-EM structures of Arabidopsis SLAC1 WT and its phosphomimetic mutants in open and closed states. Comparison of the open structure with the closed ones reveals the structural basis for opening of the conductance pore. Multiple phosphorylation of an intracellular domain (ICD) causes dissociation of ICD from the transmembrane domain. A conserved, positively-charged sequence motif in the intracellular loop 2 (ICL2) seems to be capable of sensing of the negatively charged phosphorylated ICD. Interactions between ICL2 and ICD drive drastic conformational changes, thereby widening the pore. From our results we propose that SLAC1 operates by a mechanism combining the binding-activation and inhibition-release models. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34303.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-34303-v30.xml emd-34303.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_34303_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_34303.png | 50.5 KB | ||
Masks | emd_34303_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-34303.cif.gz | 6.6 KB | ||
Others | emd_34303_half_map_1.map.gz emd_34303_half_map_2.map.gz | 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34303 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34303 | HTTPS FTP |
-Validation report
Summary document | emd_34303_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_34303_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_34303_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_34303_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34303 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34303 | HTTPS FTP |
-Related structure data
Related structure data | 8gw6MC 8gw7C 8j0jC 8j1eC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34303.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34303_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34303_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34303_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Trimer of closed state AtSLAC1 6D mutant with sfGFP tag in GDN an...
Entire | Name: Trimer of closed state AtSLAC1 6D mutant with sfGFP tag in GDN and CHS micelle |
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Components |
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-Supramolecule #1: Trimer of closed state AtSLAC1 6D mutant with sfGFP tag in GDN an...
Supramolecule | Name: Trimer of closed state AtSLAC1 6D mutant with sfGFP tag in GDN and CHS micelle type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 280 KDa |
-Macromolecule #1: Guard cell S-type anion channel SLAC1,Green fluorescent protein (...
Macromolecule | Name: Guard cell S-type anion channel SLAC1,Green fluorescent protein (Fragment) type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 94.016984 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MERKQSNAHS TFADINEVED EAEQELQQQE NNNNKRFSGN RGPNRGKQRP FRGFSRQVSL EDGFDVLNRE SRERDDKKSL PRSGRSFGG FESGGIINGG DGRKTDFDMF RTKSTLSKQK SLLPDIIRER DIENSLRTED GETKDDDINE NVDAGRYFAA L RGPELDEV ...String: MERKQSNAHS TFADINEVED EAEQELQQQE NNNNKRFSGN RGPNRGKQRP FRGFSRQVSL EDGFDVLNRE SRERDDKKSL PRSGRSFGG FESGGIINGG DGRKTDFDMF RTKSTLSKQK SLLPDIIRER DIENSLRTED GETKDDDINE NVDAGRYFAA 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 HHGSEN LYF QSMSKGEELF TGVVPILVEL DGDVNGHKFS VRGEGEGDAT NGKLTLKFIC TTGKLPVPWP TLVTTLTYGV QCFSRYP DH MKRHDFFKSA MPEGYVQERT ISFKDDGTYK TRAEVKFEGD TLVNRIELKG IDFKEDGNIL GHKLEYNFNS HNVYITAD K QKNGIKANFK IRHNVEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSTQSV LSKDPNEKRD HMVLLEFVTA AGITHGMDE LYKYPYDVPD YAGGGSHHHH HHHHHH UniProtKB: Guard cell S-type anion channel SLAC1, Green fluorescent protein |
-Macromolecule #2: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #3: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: Y01 |
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Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.3 mg/mL | ||||||||||||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 14 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |