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- EMDB-32086: The malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5) -

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Basic information

Entry
Database: EMDB / ID: EMD-32086
TitleThe malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5)
Map datathe malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5)
Sample
  • Complex: the malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5)
    • Protein or peptide: Aluminum-activated malate transporter 1
  • Ligand: (2S)-2-hydroxybutanedioic acid
KeywordsALMT1 / Aluminum Resistance / malate transport / TRANSPORT PROTEIN
Function / homologymalate transmembrane transport / malate transmembrane transporter activity / Aluminum-activated malate transporter / Aluminium activated malate transporter / response to aluminum ion / monoatomic ion transmembrane transport / plasma membrane / Aluminum-activated malate transporter 1
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang JQ
Funding support China, 4 items
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
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 19, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vq5
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32086.png

Downloads & links

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Map

FileDownload / File: emd_32086.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthe malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 180 pix.
= 182.52 Å		1.01 Å/pix.
x 180 pix.
= 182.52 Å		1.01 Å/pix.
x 180 pix.
= 182.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.08282767 - 0.13189277
Average (Standard dev.)-0.00005646041 (±0.004979492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 182.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z182.520182.520182.520
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0830.132-0.000

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Supplemental data

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Sample components

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Entire : the malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5)

EntireName: the malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5)
Components
  • Complex: the malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5)
    • Protein or peptide: Aluminum-activated malate transporter 1
  • Ligand: (2S)-2-hydroxybutanedioic acid

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Supramolecule #1: the malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5)

SupramoleculeName: the malate-bound AtALMT1 structure at pH 7.5 (ALMT1malate/pH7.5)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Aluminum-activated malate transporter 1

MacromoleculeName: Aluminum-activated malate transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 56.833668 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEKVREIVRE GIRVGNEDPR RIIHAFKVGL ALVLVSSFYY YQPFGPFTDY FGINAMWAVM TVVVVFEFSV GATLGKGLNR GVATLVAGG LGIGAHQLAR LSGATVEPIL LVMLVFVQAA LSTFVRFFPW VKTKFDYGIL IFILTFALIS LSGFRDEEIM D LAESRLST ...String:
MEKVREIVRE GIRVGNEDPR RIIHAFKVGL ALVLVSSFYY YQPFGPFTDY FGINAMWAVM TVVVVFEFSV GATLGKGLNR GVATLVAGG LGIGAHQLAR LSGATVEPIL LVMLVFVQAA LSTFVRFFPW VKTKFDYGIL IFILTFALIS LSGFRDEEIM D LAESRLST VVIGGVSCIL ISIFVCPVWA GQDLHSLLAS NFDTLSHFLQ DFGDEYFEAR EKGDYKVVEK RKKNLERYKS VL DSKSDEE ALANYAEWEP PHGQFRFRHP WKQYVAVGAL LRQCAYRIDA LNSYINSDFQ IPVDIKKKLE TPLRRMSSES GNS MKEMSI SLKQMIKSSS SDIHVSNSQA ACKSLSTLLK SGILNDVEPL QMISLMTTVS MLIDIVNLTE KISESVHELA SAAR FKNKM RPTVLYEKSD SGSIGRAMPI DSHEDHHVVT VLHDVDNDRS NNVDDSRGGS SQDSCHHVAI KIVDDNSNHE KHEDG EIHV HTLSNGHLQL EGGSSGGWSH PQFEK

UniProtKB: Aluminum-activated malate transporter 1

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Macromolecule #2: (2S)-2-hydroxybutanedioic acid

MacromoleculeName: (2S)-2-hydroxybutanedioic acid / type: ligand / ID: 2 / Number of copies: 1 / Formula: LMR
Molecular weightTheoretical: 134.087 Da
Chemical component information

ChemComp-LMR:
(2S)-2-hydroxybutanedioic acid

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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

Concentration4.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE
DetailsFor the sample of AtALMT1 bound to malate (ALMT1malate/pH7.5), the peak fractions after SEC were mixed with malate to a final concentration of 10 mM

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: the ALMT1malate/pH7.5 model was built according to the reference ALMT1apo/pH5 model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67301
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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