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- PDB-7lzi: Structure of the glutamate receptor-like channel AtGLR3.4 -

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Basic information

Entry
Database: PDB / ID: 7lzi
TitleStructure of the glutamate receptor-like channel AtGLR3.4
ComponentsGlutamate receptor 3.4
KeywordsTRANSPORT 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 / plastid / ligand-gated monoatomic ion channel activity / cellular response to cold / chloroplast / cellular response to amino acid stimulus / calcium-mediated signaling / cellular response to mechanical stimulus ...cellular response to acetate / chloroplast membrane / glutamate receptor activity / plastid / ligand-gated monoatomic ion channel activity / cellular response to cold / chloroplast / cellular response to amino acid stimulus / calcium-mediated signaling / cellular response to mechanical stimulus / response to wounding / calcium channel activity / calcium ion transport / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, plant / Plant glutamate receptor, periplasmic ligand-binding domain / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate receptor 3.4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.39 Å
AuthorsGangwar, S.P. / Green, M.N. / Sobolevsky, A.I.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA206573 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS083660 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS107253 United States
National Science Foundation (NSF, United States)1818086 United States
CitationJournal: 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
DepositionMar 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Glutamate receptor 3.4
B: Glutamate receptor 3.4
C: Glutamate receptor 3.4
D: Glutamate receptor 3.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,55612
Polymers429,2704
Non-polymers2,2868
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glutamate receptor 3.4 / AtGLR3.4 / Glutamate receptor-like protein 3.4 / Ligand-gated ion channel 3.4


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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: GLR3.4 / Type: COMPLEX
Details: Map displaying ligand binding and trans-membrane domain
Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S-GnTi / Plasmid: BacMam
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTrisC4H11NO31
2150 mMSodium ChlorideNaCl1
30.05 %DigitoninC56H92O291
SpecimenConc.: 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 supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationInstrument: 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.

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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
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 58 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2Leginonimage acquisition
4GctfCTF correction
7Coot0.9.2model fitting
9PHENIXmodel refinement
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 2161194
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 174044 / Symmetry type: POINT

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