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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23606 | |||||||||||||||
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Title | Structure of the glutamate receptor-like channel AtGLR3.4 | |||||||||||||||
![]() | GLR3.4 full length | |||||||||||||||
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Function / homology | ![]() cellular response to acetate / chloroplast membrane / glutamate receptor activity / cellular response to cold / plastid / ligand-gated monoatomic ion channel activity / cellular response to amino acid stimulus / chloroplast / calcium-mediated signaling / cellular response to mechanical stimulus ...cellular response to acetate / chloroplast membrane / glutamate receptor activity / cellular response to cold / plastid / ligand-gated monoatomic ion channel activity / cellular response to amino acid stimulus / chloroplast / calcium-mediated signaling / cellular response to mechanical stimulus / calcium channel activity / response to wounding / calcium ion transport / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.57 Å | |||||||||||||||
![]() | Gangwar SP / Green MN / Sobolevsky AI | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 167.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.7 KB 15.7 KB | Display Display | ![]() |
Images | ![]() | 194.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7lzhMC ![]() 7lz0C ![]() 7lz1C ![]() 7lz2C ![]() 7lziC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | GLR3.4 full length | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 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 : GLR3.4
Entire | Name: GLR3.4 |
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Components |
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-Supramolecule #1: GLR3.4
Supramolecule | Name: GLR3.4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Map displaying Amino-terminal, ligand binding, and transmembrane domain |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Glutamate receptor 3.4
Macromolecule | Name: Glutamate receptor 3.4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 107.317383 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGFLVMIREV SMAKAIRVVL LCVSVLWVVP KECACRSNFS RNSSSSSSSS LRPLRQRPSS VNVGALFTYD SFIGRAAKPA VKAAMDDVN ADQSVLKGIK LNIIFQDSNC SGFIGTMGAL QLMENKVVAA IGPQSSGIAH MISYVANELH VPLLSFGATD P TLSSLQFP ...String: MGFLVMIREV SMAKAIRVVL LCVSVLWVVP KECACRSNFS RNSSSSSSSS LRPLRQRPSS VNVGALFTYD SFIGRAAKPA VKAAMDDVN ADQSVLKGIK LNIIFQDSNC SGFIGTMGAL QLMENKVVAA IGPQSSGIAH MISYVANELH VPLLSFGATD P TLSSLQFP YFLRTTQNDY FQMHAIADFL SYSGWRQVIA IFVDDECGRN GISVLGDVLA KKRSRISYKA AITPGADSSS IR DLLVSVN LMESRVFVVH VNPDSGLNVF SVAKSLGMMA SGYVWIATDW LPTAMDSMEH VDSDTMDLLQ GVVAFRHYTI ESS VKRQFM ARWKNLRPND GFNSYAMYAY DSVWLVARAL DVFFRENNNI TFSNDPNLHK TNGSTIQLSA LSVFNEGEKF MKII LGMNH TGVTGPIQFD SDRNRVNPAY EVLNLEGTAP RTVGYWSNHS GLSVVHPETL YSRPPNTSTA NQRLKGIIYP GEVTK PPRG WVFPNNGKPL RIGVPNRVSY TDYVSKDKNP PGVRGYCIDV FEAAIELLPY PVPRTYILYG DGKRNPSYDN LVNEVV ADN FDVAVGDITI VTNRTRYVDF TQPFIESGLV VVAPVKEAKS SPWSFLKPFT IEMWAVTGGF FLFVGAMVWI LEHRFNQ EF RGPPRRQLIT IFWFSFSTMF FSHRENTVSS LGRFVLIIWL FVVLIINSSY TASLTSILTI RQLTSRIEGI DSLVTSNE P IGVQDGTFAR NYLINELNIL PSRIVPLKDE EQYLSALQRG PNAGGVAAIV DELPYIEVLL TNSNCKFRTV GQEFTRTGW GFAFQRDSPL AVDMSTAILQ LSEEGELEKI HRKWLNYKHE CSMQISNSED SQLSLKSFWG LFLICGITCF MALTVFFWRV FWQYQRLLP ESADEERAGE VSEPSRSGRG SRAPSFKELI KVVDKREAEI KEILKQKSSK KLKSTQSAAG TSQSQHGEIT |
-Macromolecule #3: GLUTAMIC ACID
Macromolecule | Name: GLUTAMIC ACID / type: ligand / ID: 3 / Number of copies: 4 / Formula: GLU |
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Molecular weight | Theoretical: 147.129 Da |
Chemical component information | ![]() ChemComp-GLU: |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 8 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #5: GLUTATHIONE
Macromolecule | Name: GLUTATHIONE / type: ligand / ID: 5 / Number of copies: 4 / Formula: GSH |
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Molecular weight | Theoretical: 307.323 Da |
Chemical component information | ![]() ChemComp-GSH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.5 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 1mM L-Glutamate was added to the purified protein and incubated on ice for 30 min before specimen preparation.. | ||||||||||||
Details | Protein extracted and reconstituted in a detergent micelle |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Average exposure time: 2.5 sec. / Average electron dose: 58.0 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 |