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- PDB-7lz1: Structure of glutamate receptor-like channel GLR3.4 ligand-bindin... -

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Basic information

Entry
Database: PDB / ID: 7lz1
TitleStructure of glutamate receptor-like channel GLR3.4 ligand-binding domain in complex with serine
ComponentsGlutamate receptor 3.4
KeywordsMEMBRANE PROTEIN / Arabidopsis thaliana / Ion-Channel / glutamate receptor-like channel (GLR) / Ligand binding domain
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 / response to wounding / cellular response to mechanical stimulus / 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
SERINE / Glutamate receptor 3.4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 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 8, 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,29910
Polymers89,6033
Non-polymers6967
Water3,693205
1
A: Glutamate receptor 3.4
hetero molecules

A: Glutamate receptor 3.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1306
Polymers59,7352
Non-polymers3944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
2
B: Glutamate receptor 3.4
C: Glutamate receptor 3.4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2347
Polymers59,7352
Non-polymers4985
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.509, 74.509, 507.975
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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: 29867.660 Da / Num. of mol.: 3 / Fragment: UNP residues 492-601,709-842
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GLR3.4, GLR4, GLUR3, At1g05200, YUP8H12.19 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Origami (DE3) / References: UniProt: Q8GXJ4
#2: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 45.85 % / Description: small octagonal crystals
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 2 M ammonium sulfate / Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 13, 2020
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.51→72.57 Å / Num. obs: 133111 / % possible obs: 100 % / Redundancy: 15.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.023 / Rrim(I) all: 0.089 / Net I/σ(I): 15.4 / Num. measured all: 2020815 / Scaling rejects: 222
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.51-1.5414.31.4869216264580.5240.4041.5411.5100
8.27-72.5712.40.0381328210700.9980.0110.0443.399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DENZOdata reduction
PHASERphasing
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7LZ0

7lz0


Resolution: 1.51→64.61 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.744 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2323 6610 5 %RANDOM
Rwork0.2023 ---
obs0.2038 126247 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.81 Å2 / Biso mean: 26.481 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.11 Å20 Å2
2--0.23 Å2-0 Å2
3----0.74 Å2
Refinement stepCycle: final / Resolution: 1.51→64.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5862 0 42 205 6109
Biso mean--37.06 29.52 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136025
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175693
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.6498208
X-RAY DIFFRACTIONr_angle_other_deg1.4451.57813103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3555746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.33222.508323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08315975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9771542
X-RAY DIFFRACTIONr_chiral_restr0.0870.2788
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021365
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 478 -
Rwork0.306 9177 -
all-9655 -
obs--99.98 %

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