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- PDB-6vea: Structure of the Glutamate-Like Receptor GLR3.2 ligand-binding do... -

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Basic information

Entry
Database: PDB / ID: 6vea
TitleStructure of the Glutamate-Like Receptor GLR3.2 ligand-binding domain in complex with Glycine
ComponentsGlutamate receptor 3.2
KeywordsMEMBRANE PROTEIN / ligand-binding domain / Glutamate like receptor / Ion channel / Arabidopsis
Function / homology
Function and homology information


glutamate receptor activity / ligand-gated monoatomic ion channel activity / calcium-mediated signaling / cellular response to amino acid stimulus / calcium channel activity / calcium ion transport / signaling receptor activity / 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 / 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
BETA-MERCAPTOETHANOL / GLYCINE / Glutamate receptor 3.2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsGangwar, S.P. / Green, M.N. / Yoder, J.B. / Sobolevsky, A.I.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS083660 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS107253 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA206573 United States
National Science Foundation (NSF, United States)1818213 United States
CitationJournal: Structure / Year: 2021
Title: Structure of the Arabidopsis Glutamate Receptor-like Channel GLR3.2 Ligand-Binding Domain.
Authors: Gangwar, S.P. / Green, M.N. / Michard, E. / Simon, A.A. / Feijo, J.A. / Sobolevsky, A.I.
History
DepositionDec 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Glutamate receptor 3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0325
Polymers33,7781
Non-polymers2544
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-10 kcal/mol
Surface area11320 Å2
Unit cell
Length a, b, c (Å)47.389, 64.370, 75.933
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate receptor 3.2 / AtGluR2 / Ligand-gated ion channel 3.2


Mass: 33778.094 Da / Num. of mol.: 1 / Fragment: ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GLR3.2, GLUR2, At4g35290, F23E12.150 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: Q93YT1
#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H5NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 22 % PEG 4000, 0.1 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.58→47.39 Å / Num. obs: 32133 / % possible obs: 99.2 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Net I/σ(I): 14.9 / Num. measured all: 146995 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.58-1.613.70.6122.115530.6960.3560.71398.7
8.65-47.394.80.0292100.9990.0140.03391.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VE8

6ve8


Resolution: 1.58→40.23 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.601 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 1573 4.9 %RANDOM
Rwork0.1575 ---
obs0.1588 30524 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.87 Å2 / Biso mean: 19.238 Å2 / Biso min: 10.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å2-0 Å2
2---0.63 Å20 Å2
3---1.23 Å2
Refinement stepCycle: final / Resolution: 1.58→40.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1847 0 14 191 2052
Biso mean--34.34 29.67 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131898
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171776
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.6392572
X-RAY DIFFRACTIONr_angle_other_deg1.5471.5744095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7515239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46621.3100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32115298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0711515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022155
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02426
LS refinement shellResolution: 1.58→1.621 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 118 -
Rwork0.24 2219 -
all-2337 -
obs--99.03 %

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