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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-32085 | |||||||||||||||
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Title | The apo-state AtALMT1 structure at pH 7.5(ALMT1apo/pH7.5) | |||||||||||||||
![]() | the apo-state AtALMT1 structure at pH 5 | |||||||||||||||
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![]() | ALMT1 / Aluminum Resistance / malate transport / TRANSPORT PROTEIN | |||||||||||||||
Function / homology | malate 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![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||
![]() | Wang JQ | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 20.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.3 KB 10.3 KB | Display Display | ![]() |
Images | ![]() | 33.6 KB | ||
Filedesc metadata | ![]() | 5.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vq4MC ![]() 7vojC ![]() 7vq3C ![]() 7vq5C ![]() 7vq7C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | the apo-state AtALMT1 structure at pH 5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : the apo-state AtALMT1 structure at pH 7.5(ALMT1apo/pH7.5)
Entire | Name: the apo-state AtALMT1 structure at pH 7.5(ALMT1apo/pH7.5) |
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Components |
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-Supramolecule #1: the apo-state AtALMT1 structure at pH 7.5(ALMT1apo/pH7.5)
Supramolecule | Name: the apo-state AtALMT1 structure at pH 7.5(ALMT1apo/pH7.5) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Aluminum-activated malate transporter 1
Macromolecule | Name: Aluminum-activated malate transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 56.833668 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | 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 model | Type of model: OTHER Details: the ALMT1apo/pH7.5 model was built according to the reference ALMT1apo/pH5 model |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54315 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |