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- PDB-6r89: Structure of Arabidopsis thaliana GLR3.3 ligand-binding domain in... -

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Basic information

Entry
Database: PDB / ID: 6r89
TitleStructure of Arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-cysteine
ComponentsGlutamate receptor 3.3,Glutamate receptor 3.3
KeywordsMEMBRANE PROTEIN / glutamate receptor-like / amino acid-binding
Function / homology
Function and homology information


induced systemic resistance, jasmonic acid mediated signaling pathway / gravitropism / glutamate receptor activity / ligand-gated monoatomic ion channel activity / defense response to fungus / calcium-mediated signaling / cellular response to amino acid stimulus / calcium channel activity / response to wounding / calcium ion transport ...induced systemic resistance, jasmonic acid mediated signaling pathway / gravitropism / glutamate receptor activity / ligand-gated monoatomic ion channel activity / defense response to fungus / calcium-mediated signaling / cellular response to amino acid stimulus / calcium channel activity / response to wounding / calcium ion transport / cell-cell signaling / innate immune response / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, plant / Plant glutamate receptor, periplasmic ligand-binding domain / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Ionotropic glutamate receptor, plant / Plant glutamate receptor, periplasmic ligand-binding domain / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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
CYSTEINE / Glutamate receptor 3.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsAlfieri, A. / Pederzoli, R. / Costa, A.
Funding support Italy, 2items
OrganizationGrant numberCountry
Other governmentItalian Ministry of Education, University and Research - FIRB 2010 - RBFR10S1LJ_001 grant Italy
Other governmentUniversity of Milan (Italy) - PIANO DI SVILUPPO DI ATENEO 2017 Italy
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: The structural bases for agonist diversity in anArabidopsis thalianaglutamate receptor-like channel.
Authors: Alfieri, A. / Doccula, F.G. / Pederzoli, R. / Grenzi, M. / Bonza, M.C. / Luoni, L. / Candeo, A. / Romano Armada, N. / Barbiroli, A. / Valentini, G. / Schneider, T.R. / Bassi, A. / Bolognesi, ...Authors: Alfieri, A. / Doccula, F.G. / Pederzoli, R. / Grenzi, M. / Bonza, M.C. / Luoni, L. / Candeo, A. / Romano Armada, N. / Barbiroli, A. / Valentini, G. / Schneider, T.R. / Bassi, A. / Bolognesi, M. / Nardini, M. / Costa, A.
History
DepositionApr 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Feb 5, 2020Group: Refinement description / Category: refine_ls_shell / Item: _refine_ls_shell.d_res_low
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 3.3,Glutamate receptor 3.3
B: Glutamate receptor 3.3,Glutamate receptor 3.3
C: Glutamate receptor 3.3,Glutamate receptor 3.3
D: Glutamate receptor 3.3,Glutamate receptor 3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,44112
Polymers107,7834
Non-polymers6588
Water6,431357
1
A: Glutamate receptor 3.3,Glutamate receptor 3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1134
Polymers26,9461
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor 3.3,Glutamate receptor 3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0672
Polymers26,9461
Non-polymers1211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutamate receptor 3.3,Glutamate receptor 3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1944
Polymers26,9461
Non-polymers2493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Glutamate receptor 3.3,Glutamate receptor 3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0672
Polymers26,9461
Non-polymers1211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.661, 98.544, 114.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glutamate receptor 3.3,Glutamate receptor 3.3 / Ligand-gated ion channel 3.3


Mass: 26945.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GLR3.3, At1g42540, T8D8.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9C8E7

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Non-polymers , 5 types, 365 molecules

#2: Chemical
ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 100 mM HEPES pH 7.5, sodium citrate tribasic 1.4 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→49.4 Å / Num. obs: 38874 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.986 / Rmerge(I) obs: 0.272 / Rpim(I) all: 0.113 / Rrim(I) all: 0.295 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.66.91.61343390.5780.6621.745100
9.01-49.45.80.0589390.9990.0250.06399.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.604
Highest resolutionLowest resolution
Rotation49.39 Å2.56 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
Aimless0.7.3data scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R85
Resolution: 2.5→49.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.357 / SU ML: 0.211 / SU R Cruickshank DPI: 0.5391 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.4 / ESU R Free: 0.241
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 2108 4.8 %RANDOM
Rwork0.1882 ---
obs0.1901 36927 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 125.62 Å2 / Biso mean: 35.47 Å2 / Biso min: 12.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å20 Å20 Å2
2---0.92 Å20 Å2
3----1.83 Å2
Refinement stepCycle: final / Resolution: 2.5→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7400 0 9 357 7766
Biso mean--42.25 32.28 -
Num. residues----964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137599
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177126
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.64610317
X-RAY DIFFRACTIONr_angle_other_deg1.2621.57416530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36922.35366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.279151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6811544
X-RAY DIFFRACTIONr_chiral_restr0.1550.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021578
LS refinement shellResolution: 2.5→2.566 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 147 -
Rwork0.345 3043 -
all-3190 -
obs--99.97 %

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