+Open data
-Basic information
Entry | Database: PDB / ID: 7lzh | |||||||||||||||
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Title | Structure of the glutamate receptor-like channel AtGLR3.4 | |||||||||||||||
Components | Glutamate receptor 3.4 | |||||||||||||||
Keywords | TRANSPORT PROTEIN / Arabidopsis thaliana / Ion-Channel / glutamate receptor-like channel (GLR) | |||||||||||||||
Function / homology | Function and homology information cellular response to acetate / chloroplast membrane / glutamate receptor activity / cellular response to cold / plastid / ligand-gated monoatomic ion channel activity / chloroplast / cellular response to amino acid stimulus / calcium-mediated signaling / calcium channel activity ...cellular response to acetate / chloroplast membrane / glutamate receptor activity / cellular response to cold / plastid / ligand-gated monoatomic ion channel activity / chloroplast / cellular response to amino acid stimulus / calcium-mediated signaling / calcium channel activity / cellular response to mechanical stimulus / response to wounding / calcium ion transport / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å | |||||||||||||||
Authors | Gangwar, S.P. / Green, M.N. / Sobolevsky, A.I. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Mol Cell / Year: 2021 Title: Structure of the Arabidopsis thaliana glutamate receptor-like channel GLR3.4. Authors: Marriah N Green / Shanti Pal Gangwar / Erwan Michard / Alexander A Simon / Maria Teresa Portes / Juan Barbosa-Caro / Michael M Wudick / Michael A Lizzio / Oleg Klykov / Maria V Yelshanskaya ...Authors: Marriah N Green / Shanti Pal Gangwar / Erwan Michard / Alexander A Simon / Maria Teresa Portes / Juan Barbosa-Caro / Michael M Wudick / Michael A Lizzio / Oleg Klykov / Maria V Yelshanskaya / José A Feijó / Alexander I Sobolevsky / Abstract: Glutamate receptor-like channels (GLRs) play vital roles in various physiological processes in plants, such as wound response, stomatal aperture control, seed germination, root development, innate ...Glutamate receptor-like channels (GLRs) play vital roles in various physiological processes in plants, such as wound response, stomatal aperture control, seed germination, root development, innate immune response, pollen tube growth, and morphogenesis. Despite the importance of GLRs, knowledge about their molecular organization is limited. Here we use X-ray crystallography and single-particle cryo-EM to solve structures of the Arabidopsis thaliana GLR3.4. Our structures reveal the tetrameric assembly of GLR3.4 subunits into a three-layer domain architecture, reminiscent of animal ionotropic glutamate receptors (iGluRs). However, the non-swapped arrangement between layers of GLR3.4 domains, binding of glutathione through S-glutathionylation of cysteine C205 inside the amino-terminal domain clamshell, unique symmetry, inter-domain interfaces, and ligand specificity distinguish GLR3.4 from representatives of the iGluR family and suggest distinct features of the GLR gating mechanism. Our work elaborates on the principles of GLR architecture and symmetry and provides a molecular template for deciphering GLR-dependent signaling mechanisms in plants. | |||||||||||||||
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 | 7lzh.cif.gz | 555.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lzh.ent.gz | 467.7 KB | Display | PDB format |
PDBx/mmJSON format | 7lzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lzh_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7lzh_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7lzh_validation.xml.gz | 85.9 KB | Display | |
Data in CIF | 7lzh_validation.cif.gz | 130.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/7lzh ftp://data.pdbj.org/pub/pdb/validation_reports/lz/7lzh | HTTPS FTP |
-Related structure data
Related structure data | 23606MC 7lz0C 7lz1C 7lz2C 7lziC 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: 107317.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GLR3.4, GLR4, GLUR3, At1g05200, YUP8H12.19 / Plasmid: BacMam / Cell line (production host): HEK293S-GnTi / Production host: Homo sapiens (human) / References: UniProt: Q8GXJ4 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-GLU / #4: Sugar | ChemComp-NAG / #5: Chemical | ChemComp-GSH / Has ligand of interest | Y | |
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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: GLR3.4 / Type: COMPLEX Details: Map displaying Amino-terminal, ligand binding, and transmembrane domain Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Arabidopsis thaliana (thale cress) | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293S-GnTi / Plasmid: BacMam | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Protein extracted and reconstituted in a detergent micelle | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: 1mM L-Glutamate was added to the purified protein and incubated on ice for 30 min before specimen preparation. |
-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: 2.5 sec. / Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2161194 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110630 / Symmetry type: POINT |