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- PDB-8zvf: AtALMT9 plus high malate in low pH -

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Basic information

Entry
Database: PDB / ID: 8zvf
TitleAtALMT9 plus high malate in low pH
ComponentsAluminum-activated malate transporter 9
KeywordsTRANSPORT PROTEIN / CHANNEL
Function / homologymalate transport / Aluminum-activated malate transporter / Aluminium activated malate transporter / plant-type vacuole membrane / monoatomic anion channel activity / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / Aluminum-activated malate transporter 9
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsGong, D.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Aluminum-activated malate transporter 9
B: Aluminum-activated malate transporter 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,3134
Polymers134,2422
Non-polymers1,0712
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Aluminum-activated malate transporter 9 / AtALMT9


Mass: 67121.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ALMT9, At3g18440, MYF24.16 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9LS46
#2: Chemical ChemComp-PX2 / 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE


Mass: 535.671 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H52O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dimer of AtALMT9 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 5.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 71 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118165 / Symmetry type: POINT

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