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- EMDB-63695: At 2S1+S3-tRNA trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-63695
TitleAt 2S1+S3-tRNA trimer
Map data
Sample
  • Organelle or cellular component: At S1+2S3 trimer
    • Protein or peptide: S-type anion channel SLAH3
    • Protein or peptide: S-type anion channel SLAH1
    • RNA: RNA (75-MER)
KeywordsAt 2S1+S3-tRNA trimer / MEMBRANE PROTEIN/RNA / MEMBRANE PROTEIN-RNA complex
Function / homology
Function and homology information


voltage-gated monoatomic anion channel activity / intracellular monoatomic ion homeostasis / response to water deprivation / chloride transport / response to salt stress / 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
S-type anion channel SLAH1 / S-type anion channel SLAH3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsZhang SS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030056 China
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the coordinated regulation of the SLAH family in Arabidopsis thaliana.
Authors: Sensen Zhang / Xueying Huang / Xiaojuan Wang / Boya Qi / Kaiwen Yang / Chang Liu / Ruochong Li / Xudong Chen / Jingbo Yi / Jian Yin / Maofei Chen / Botong Liu / Jiayi Fan / Tao Liu / Zhilin ...Authors: Sensen Zhang / Xueying Huang / Xiaojuan Wang / Boya Qi / Kaiwen Yang / Chang Liu / Ruochong Li / Xudong Chen / Jingbo Yi / Jian Yin / Maofei Chen / Botong Liu / Jiayi Fan / Tao Liu / Zhilin Hao / Kun Cui / Ni Xiao / Yingcai Song / Yujie Li / Di Wu / Tiancong Qi / Jian Mao / Bing Zhang / Maojun Yang / Jianping Xie / Zhiqiang Liu /
Abstract: S-type anion channel homologs (SLAH) are widely expressed in various plant tissues and play a key role in anion transport, which is crucial for plant adaptation to both biotic and abiotic stresses. ...S-type anion channel homologs (SLAH) are widely expressed in various plant tissues and play a key role in anion transport, which is crucial for plant adaptation to both biotic and abiotic stresses. In this study, we employ cryo-electron microscopy (cryo-EM) to analyze four SLAH channel complexes from Arabidopsis thaliana: the homotrimeric SLAH3 channel, the 2SLAH1 + SLAH3+tRNA complex, the 1SLAH1 + 2SLAH3 complex, and the 3SLAH1+tRNA complex. Critically, our studies reveal that tRNA directly binds to and occupies the intracellular entrance of the SLAH1 homotrimer and the 2SLAH1 + SLAH3 heterocomplex. Electrophysiological experiments confirm tRNA's role as a potent inhibitory regulatory subunit: RNase-mediated tRNA degradation robustly activates SLAH1 currents, while targeted mutagenesis of SLAH1 tRNA-interacting residues phenocopy this activation and enhanced ABA-induced stomatal closure. Combining with structural biology, electrophysiology, and biochemistry, we comprehensively examine the key residues in SLAH1 and SLAH3 that are responsible for the anion permeation. This mechanistic advancement provides a deeper understanding of the molecular basis for plant stress tolerance and identifies specific molecular targets for future engineering crops.
History
DepositionMar 11, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63695.png

Downloads & links

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Map

FileDownload / File: emd_63695.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.148
Minimum - Maximum-2.2663176 - 3.9045315
Average (Standard dev.)0.00009726108 (±0.073513545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63695_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_63695_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : At S1+2S3 trimer

EntireName: At S1+2S3 trimer
Components
  • Organelle or cellular component: At S1+2S3 trimer
    • Protein or peptide: S-type anion channel SLAH3
    • Protein or peptide: S-type anion channel SLAH1
    • RNA: RNA (75-MER)

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Supramolecule #1: At S1+2S3 trimer

SupramoleculeName: At S1+2S3 trimer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: S-type anion channel SLAH3

MacromoleculeName: S-type anion channel SLAH3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 72.421453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEEKPNYVIQ VEEELPTLLR KATTEEMVGF DNYKENGHPF PHSISRFHPS HASTTTLNGQ ETSRSIDTME AHHHNYNETT PWTHQRKPS ISMPTSPNVL MISDPTTSLS SENHKNSGST GKSVKFLSQP MTKVSSLYIE SGNGDDDRRQ SHDNHHHHLH R QHQSGHHQ ...String:
MEEKPNYVIQ VEEELPTLLR KATTEEMVGF DNYKENGHPF PHSISRFHPS HASTTTLNGQ ETSRSIDTME AHHHNYNETT PWTHQRKPS ISMPTSPNVL MISDPTTSLS SENHKNSGST GKSVKFLSQP MTKVSSLYIE SGNGDDDRRQ SHDNHHHHLH R QHQSGHHQ NQNQAANKLK DNRYNSFKTW SGKLERQFTR KPASVEPEAP NRNNQNLNTN EAMPVDRYYD ALEGPELETL RP QEEIVLP NDKKWPFLLR YPISTFGMCL GVSSQAIMWK TLATAEPTKF LHVPLWINQG LWFISVALIL TIATIYLLKI ILF FEAVRR EYYHPIRINF FFAPFISLLF LALGVPPSII TDLPHFLWYL LMFPFICLEL KIYGQWMSGG QRRLSRVANP TNHL SVVGN FVGALLGASM GLREGPIFFY AVGMAHYLVL FVTLYQRLPT NETLPKDLHP VFFLFVAAPS VASMAWAKVT GSFDY GSKV CYFIAIFLYF SLAVRINFFR GIKFSLSWWA YTFPMTGAAI ATIRYATVVK STMTQIMCVV LCAIATLVVF ALLVTT IIH AFVLRDLFPN DLAIAISNRP RPKQNSQHRW LDQLRNVSSE NIENYLKFTD SDSSQSNDVE ACNGKTQESD SS

UniProtKB: S-type anion channel SLAH3

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Macromolecule #2: S-type anion channel SLAH1

MacromoleculeName: S-type anion channel SLAH1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 43.44532 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEIPRQEIHI EIDNSIPSSK EFKTGLADAK PVVLMSALRS LHAGYFRISL SLCSQALLWK IMIAPESPSM SHMHSKLPSM AFHLLWYLA LVTQVSLCFL YALKCIFFFD KVKEEFLHYI GVNYLYAPSI SWLLMLQSAP MMEPNSVLYQ TLFWIFAVPV L TLDIKLYG ...String:
MEIPRQEIHI EIDNSIPSSK EFKTGLADAK PVVLMSALRS LHAGYFRISL SLCSQALLWK IMIAPESPSM SHMHSKLPSM AFHLLWYLA LVTQVSLCFL YALKCIFFFD KVKEEFLHYI GVNYLYAPSI SWLLMLQSAP MMEPNSVLYQ TLFWIFAVPV L TLDIKLYG QWFTTEKRFL SMLANPASQV SVIANLVAAR GAAEMGWNEC ALCMFSLGMV HYLVIFVTLY QRLPGGNNFP AK LRPIFFL FVAAPAMASL AWNSICGTFD AVAKMLFFLS LFIFMSLVCR PNLFKKSMKR FNVAWWAYSF PLTFLALDSV QYA QEVKDP VGSGLMLIFS SISVLIFLGM MVLTAANSNR LLRHDPVLGS ATDPKDKQKT LSLNATNQN

UniProtKB: S-type anion channel SLAH1

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Macromolecule #3: RNA (75-MER)

MacromoleculeName: RNA (75-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.108287 KDa
SequenceString:
UCUUCGGUAG UAUAGUGGUC AGUAUCCCCG CCUGUCACGC GGGAGACCGG GGUUCGAUUC CCCGCCGGAG AGCCA

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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: 7.2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 167000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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