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- EMDB-23607: Structure of the glutamate receptor-like channel AtGLR3.4 -

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Basic information

Entry
Database: EMDB / ID: EMD-23607
TitleStructure of the glutamate receptor-like channel AtGLR3.4
Map dataSubtracted map
Sample
  • Complex: GLR3.4
    • Protein or peptide: Glutamate receptor 3.4
  • Ligand: GLUTAMIC ACID
KeywordsArabidopsis thaliana / Ion-Channel / glutamate receptor-like channel (GLR) / TRANSPORT PROTEIN
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
Glutamate receptor 3.4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.39 Å
AuthorsGangwar SP / Green MN
Funding support United States, 4 items
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, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lzi
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23607.png

Downloads & links

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Map

FileDownload / File: emd_23607.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtracted map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0085 / Movie #1: 0.0085
Minimum - Maximum-0.01819264 - 0.041648787
Average (Standard dev.)0.00007864461 (±0.0010108833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z298.800298.800298.800
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0180.0420.000

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Supplemental data

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Sample components

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Entire : GLR3.4

EntireName: GLR3.4
Components
  • Complex: GLR3.4
    • Protein or peptide: Glutamate receptor 3.4
  • Ligand: GLUTAMIC ACID

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Supramolecule #1: GLR3.4

SupramoleculeName: GLR3.4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Map displaying ligand binding and trans-membrane domain
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Glutamate receptor 3.4

MacromoleculeName: Glutamate receptor 3.4 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 107.317383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

UniProtKB: Glutamate receptor 3.4

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Macromolecule #3: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 3 / Number of copies: 4 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
150.0 mMNaClSodium Chloride
0.05 %C56H92O29Digitonin
GridModel: C-flat-1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen 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..
DetailsProtein extracted and reconstituted in a detergent micelle

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

Particle selectionNumber selected: 2161194
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3kg2

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 174044
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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