+Open data
-Basic information
Entry | Database: PDB / ID: 7vq3 | ||||||||||||
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Title | The apo-state AtALMT1 structures at pH 5 (ALMT1apo/pH5) | ||||||||||||
Components | Aluminum-activated malate transporter 1 | ||||||||||||
Keywords | TRANSPORT PROTEIN / ALMT1 / Aluminum Resistance / malate transport | ||||||||||||
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 Function and homology information | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Wang, J.Q. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7vq3.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vq3.ent.gz | 115.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vq3_validation.pdf.gz | 854.1 KB | Display | wwPDB validaton report |
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Full document | 7vq3_full_validation.pdf.gz | 859.5 KB | Display | |
Data in XML | 7vq3_validation.xml.gz | 26 KB | Display | |
Data in CIF | 7vq3_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/7vq3 ftp://data.pdbj.org/pub/pdb/validation_reports/vq/7vq3 | HTTPS FTP |
-Related structure data
Related structure data | 32084MC 7vojC 7vq4C 7vq5C 7vq7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 56833.668 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ALMT1, At1g08430, T27G7.11 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9SJE9 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: the apo-state AtALMT1 structures at pH 5 (ALMT1apo/pH5) Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm |
Image recording | Average exposure time: 8 sec. / Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 187470 / Symmetry type: POINT | ||||||||||||||||||||||||
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