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- EMDB-34829: AtALMT9 plus malate -

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Basic information

Entry
Database: EMDB / ID: EMD-34829
TitleAtALMT9 plus malate
Map data
Sample
  • Complex: Dimer of AtALMT9
    • Protein or peptide: Aluminum-activated malate transporter 9
KeywordsCHANNEL / TRANSPORT PROTEIN
Function / homologymalate transport / Aluminum-activated malate transporter / Aluminium activated malate transporter / plant-type vacuole membrane / monoatomic anion channel activity / Aluminum-activated malate transporter 9
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGong DS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271254 China
CitationJournal: Cell Rep / Year: 2024
Title: Structural insight into the Arabidopsis vacuolar anion channel ALMT9 shows clade specificity.
Authors: Dandan Qian / Yaru Chai / Weiping Li / Bin Cui / Shaoquan Lin / Zhibin Wang / Chongyuan Wang / Le Qing Qu / Deshun Gong /
Abstract: The Arabidopsis thaliana aluminum-activated malate transporter 9 (AtALMT9) functions as a vacuolar chloride channel that regulates the stomatal aperture. Here, we present the cryoelectron microscopy ...The Arabidopsis thaliana aluminum-activated malate transporter 9 (AtALMT9) functions as a vacuolar chloride channel that regulates the stomatal aperture. Here, we present the cryoelectron microscopy (cryo-EM) structures of AtALMT9 in three distinct states. AtALMT9 forms a dimer, and the pore is lined with four positively charged rings. The apo-AtALMT9 state shows a putative endogenous citrate obstructing the pore, where two W120 constriction residues enclose a gate with a pore radius of approximately 1.8 Å, representing an open state. Interestingly, channel closure is solely controlled by W120. Compared to wild-type plants, the W120A mutant exhibits more sensitivity to drought stress and is unable to restore the visual phenotype on leaves upon water recovery, reflecting persistent stomatal opening. Furthermore, notable variations are noted in channel gating and substrate recognition of Glycine max ALMT12, AtALMT9, and AtALMT1. In summary, our investigation enhances comprehension of the interplay between structure and function within the ALMT family.
History
DepositionNov 22, 2022-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34829.png

Downloads & links

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Map

FileDownload / File: emd_34829.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.)
1.88 Å/pix.
x 128 pix.
= 240.64 Å		1.88 Å/pix.
x 128 pix.
= 240.64 Å		1.88 Å/pix.
x 128 pix.
= 240.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.1.08251.08251.0825
CCP4 map header1.881.881.88
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-1.7572606 - 3.793105
Average (Standard dev.)0.002687185 (±0.050901756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34829_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer of AtALMT9

EntireName: Dimer of AtALMT9
Components
  • Complex: Dimer of AtALMT9
    • Protein or peptide: Aluminum-activated malate transporter 9

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Supramolecule #1: Dimer of AtALMT9

SupramoleculeName: Dimer of AtALMT9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Aluminum-activated malate transporter 9

MacromoleculeName: Aluminum-activated malate transporter 9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 67.121008 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAKQGSFRH GILEKRERLL SNNGFSDFRF TDIESNDLLE NENCGRRTRL CCCCSCGNLS EKISGVYDDA KDVARKAWEM GVSDPRKIV FSAKIGLALT IVALLIFYQE PNPDLSRYSV WAILTVVVVF EFTIGATLSK GFNRALGTLS AGGLALGMAE L STLFGDWE ...String:
MAAKQGSFRH GILEKRERLL SNNGFSDFRF TDIESNDLLE NENCGRRTRL CCCCSCGNLS EKISGVYDDA KDVARKAWEM GVSDPRKIV FSAKIGLALT IVALLIFYQE PNPDLSRYSV WAILTVVVVF EFTIGATLSK GFNRALGTLS AGGLALGMAE L STLFGDWE EIFCTLSIFC IGFLATFMKL YPSMKAYEYG FRVFLLTYCY ILISGFRTGQ FIEVAISRFL LIALGAGVSL GV NMFIYPI WAGEDLHNLV VKNFMNVATS LEGCVNGYLR CLEYERIPSK ILTYQASEDP VYKGYRSAVE STSQEESLMS FAI WEPPHG PYKSFNYPWK NYVKLSGALK HCAFTVMALH GCILSEIQAP EERRQVFRQE LQRVGVEGAK LLRELGEKVK KMEK LGPVD LLFEVHLAAE ELQHKIDKKS YLLVNSECWE IGNRATKESE PQELLSLEDS DPPENHAPPI YAFKSLSEAV LEIPP SWGE KNHREALNHR PTFSKQVSWP ARLVLPPHLE TTNGASPLVE TTKTYESASA LSLATFASLL IEFVARLQNV VDAFKE LSQ KANFKEPEIV TTGTDVEFSG ERVGLGQKIR RCFGM

UniProtKB: Aluminum-activated malate transporter 9

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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) / 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: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143287
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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