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- PDB-6ve8: Structure of the Glutamate-Like Receptor GLR3.2 ligand-binding do... -

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Basic information

Entry
Database: PDB / ID: 6ve8
TitleStructure of the Glutamate-Like Receptor GLR3.2 ligand-binding domain in complex with Methionine
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 / cellular response to amino acid stimulus / calcium-mediated signaling / 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 / METHIONINE / Glutamate receptor 3.2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGangwar, S.P. / Green, M.N. / Yoder, J.B. / Sobolevsky, A.I.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1818213 United States
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
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)34,1335
Polymers33,7781
Non-polymers3554
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-10 kcal/mol
Surface area11020 Å2
Unit cell
Length a, b, c (Å)47.645, 65.470, 72.186
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, 1 molecules A

#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

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Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S / 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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6OS
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.46 % / Description: long Rod shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 18% PEG MME 2K, 0.1 M Ammonium sulfate

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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: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.75→72.19 Å / Num. obs: 23419 / % possible obs: 99.8 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.037 / Rrim(I) all: 0.087 / Net I/σ(I): 13.3 / Num. measured all: 124336 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.783.10.6741.812580.6550.4330.80699.1
9.09-72.194.40.0462060.9980.0230.05197.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model based on 6MMS

6mms


Resolution: 1.75→48.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.378 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 1167 5 %RANDOM
Rwork0.165 ---
obs0.1667 22200 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.31 Å2 / Biso mean: 22.065 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å2-0 Å2
2---0.71 Å20 Å2
3---1.47 Å2
Refinement stepCycle: final / Resolution: 1.75→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 20 112 1962
Biso mean--33.58 29.39 -
Num. residues----237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131887
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171773
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.6382557
X-RAY DIFFRACTIONr_angle_other_deg1.4451.5734089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1521.21299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41915300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0761515
X-RAY DIFFRACTIONr_chiral_restr0.0860.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
LS refinement shellResolution: 1.75→1.796 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 86 -
Rwork0.28 1598 -
all-1684 -
obs--98.94 %

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