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- PDB-7voj: Al-bound structure of the AtALMT1 mutant M60A -

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Basic information

Entry
Database: PDB / ID: 7voj
TitleAl-bound structure of the AtALMT1 mutant M60A
ComponentsAluminum-activated malate transporter 1
KeywordsTRANSPORT PROTEIN / ALMT1 / Aluminum Resistance / malate transport
Function / homology
Function and homology information


malate transmembrane transport / malate transmembrane transporter activity / response to aluminum ion / monoatomic ion transmembrane transport / plasma membrane
Similarity search - Function
Aluminum-activated malate transporter / Aluminium activated malate transporter
Similarity search - Domain/homology
ACETIC ACID / ALUMINUM ION / Aluminum-activated malate transporter 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWang, J.
Funding support China, 9items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0908501 China
Ministry of Science and Technology (MoST, China)2018YFA0508100 China
Ministry of Science and Technology (MoST, China)2016YFA0501100 China
National Natural Science Foundation of China (NSFC)31870724 China
National Natural Science Foundation of China (NSFC)82030108 China
National Natural Science Foundation of China (NSFC)31872796 China
National Natural Science Foundation of China (NSFC)81571127 China
National Natural Science Foundation of China (NSFC)31730006 China
National Natural Science Foundation of China (NSFC)31600606 China
CitationJournal: Cell Res / Year: 2022
Title: Structural basis of ALMT1-mediated aluminum resistance in Arabidopsis.
Authors: Jiangqin Wang / Xiafei Yu / Zhong Jie Ding / Xiaokang Zhang / Yanping Luo / Ximing Xu / Yuan Xie / Xiaoxiao Li / Tian Yuan / Shao Jian Zheng / Wei Yang / Jiangtao Guo /
Abstract: The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance. Here we present cryo-electron ...The plant aluminum (Al)-activated malate transporter ALMT1 mediates the efflux of malate to chelate the Al in acidic soils and underlies the plant Al resistance. Here we present cryo-electron microscopy (cryo-EM) structures of Arabidopsis thaliana ALMT1 (AtALMT1) in the apo, malate-bound, and Al-bound states at neutral and/or acidic pH at up to 3.0 Å resolution. The AtALMT1 dimer assembles an anion channel and each subunit contains six transmembrane helices (TMs) and six cytosolic α-helices. Two pairs of Arg residues are located in the center of the channel pore and contribute to malate recognition. Al binds at the extracellular side of AtALMT1 and induces conformational changes of the TM1-2 loop and the TM5-6 loop, resulting in the opening of the extracellular gate. These structures, along with electrophysiological measurements, molecular dynamic simulations, and mutagenesis study in Arabidopsis, elucidate the structural basis for Al-activated malate transport by ALMT1.
History
DepositionOct 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Aluminum-activated malate transporter 1
B: Aluminum-activated malate transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8418
Polymers113,5472
Non-polymers2946
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5940 Å2
ΔGint-76 kcal/mol
Surface area38960 Å2

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Components

#1: Protein Aluminum-activated malate transporter 1 / AtALMT1


Mass: 56773.551 Da / Num. of mol.: 2 / Mutation: M60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ALMT1, At1g08430, T27G7.11 / Plasmid: pEZT-BM / Cell (production host): human embryonic kidney cells / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9SJE9
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical ChemComp-AL / ALUMINUM ION


Mass: 26.982 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Al / 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: Al-bound protein sample of the AtALMT1 mutant M60A / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 120 kDa/nm / Experimental value: YES
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Cellular location: cell membrane / Organ: root / Tissue: root apex
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK-293 / Plasmid: pEZT-BM
Buffer solutionpH: 5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMSodium chlorideNacl1
250 mMSodium acetate-acetic acidNaAc-HAc1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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 / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 8 sec. / Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1RELION3particle selectionRELION autopicking program was used to automatically select particle images
4GctfCTF correctionthe CTF parameters of the micrographs were estimated using the GCTF program
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3586060
Details: about 1,000 particles were manually picked from the micrographs for 2D classification initially. Class averages representing projections of AtALMT1 in different orientations were selected ...Details: about 1,000 particles were manually picked from the micrographs for 2D classification initially. Class averages representing projections of AtALMT1 in different orientations were selected and used as templates for automated particle picking
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 216946 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT

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