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- PDB-6r8a: Structure of Arabidopsis thaliana GLR3.3 ligand-binding domain in... -

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Basic information

Entry
Database: PDB / ID: 6r8a
TitleStructure of Arabidopsis thaliana GLR3.3 ligand-binding domain in complex with L-methionine
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 / kainate selective glutamate receptor complex / 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 / modulation of chemical synaptic transmission ...induced systemic resistance, jasmonic acid mediated signaling pathway / gravitropism / kainate selective glutamate receptor complex / 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 / modulation of chemical synaptic transmission / 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
METHIONINE / Glutamate receptor 3.3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 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 1.3Jan 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)108,49910
Polymers107,7834
Non-polymers7166
Water181
1
A: Glutamate receptor 3.3,Glutamate receptor 3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1183
Polymers26,9461
Non-polymers1722
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)27,0952
Polymers26,9461
Non-polymers1491
Water0
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)27,0952
Polymers26,9461
Non-polymers1491
Water0
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)27,1913
Polymers26,9461
Non-polymers2452
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.480, 96.800, 114.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 239
2010B3 - 239
1020A3 - 238
2020C3 - 238
1030A3 - 238
2030D3 - 238
1040B3 - 238
2040C3 - 238
1050B3 - 238
2050D3 - 238
1060C3 - 243
2060D3 - 239

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#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
#2: Chemical
ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H11NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
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: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.1→49.19 Å / Num. obs: 19607 / % possible obs: 98.8 % / Redundancy: 4.3 % / CC1/2: 0.969 / Rmerge(I) obs: 0.422 / Rpim(I) all: 0.213 / Rrim(I) all: 0.475 / Net I/σ(I): 4.1 / Num. measured all: 83521
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.1-3.314.42.32435340.4521.1322.59599.6
8.77-49.193.80.0639120.9950.0360.07395.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.576
Highest resolutionLowest resolution
Rotation49.19 Å3.59 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R85

6r85


Resolution: 3.1→49.19 Å / Cor.coef. Fo:Fc: 0.867 / Cor.coef. Fo:Fc free: 0.776 / SU B: 37.242 / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.731
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3065 731 4.6 %RANDOM
Rwork0.2421 ---
obs0.245 15026 79.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.17 Å2 / Biso mean: 37.843 Å2 / Biso min: 6.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å2-0 Å2
2--0.14 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 3.1→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7108 0 6 1 7115
Biso mean--18.84 6.99 -
Num. residues----924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137539
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177086
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.64610232
X-RAY DIFFRACTIONr_angle_other_deg1.1581.57416432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.87122.308364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.489151232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2391544
X-RAY DIFFRACTIONr_chiral_restr0.0530.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028436
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021568
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A70740.11
12B70740.11
21A71330.11
22C71330.11
31A71440.11
32D71440.11
41B70310.12
42C70310.12
51B71280.1
52D71280.1
61C71590.1
62D71590.1
LS refinement shellResolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 3 -
Rwork0.324 116 -
all-119 -
obs--8.24 %

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