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- PDB-2qs1: Crystal structure of the GluR5 ligand binding core dimer in compl... -

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Basic information

Entry
Database: PDB / ID: 2qs1
TitleCrystal structure of the GluR5 ligand binding core dimer in complex with UBP315 at 1.80 Angstroms resolution
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / Cell junction / Glycoprotein / Ion transport / Ionic channel / Phosphorylation / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport
Function / homology
Function and homology information


negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / amino acid transmembrane transport / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity ...negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / amino acid transmembrane transport / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / behavioral response to pain / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / sodium ion transmembrane transport / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / potassium ion transmembrane transport / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / synaptic transmission, glutamatergic / establishment of localization in cell / positive regulation of synaptic transmission, GABAergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / presynaptic membrane / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / postsynaptic density / receptor complex / neuronal cell body / glutamatergic synapse / dendrite / synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / 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 ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / 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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-UB1 / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsAlushin, G.M. / Jane, D.E. / Mayer, M.L.
CitationJournal: Neuropharmacology / Year: 2011
Title: Binding site and ligand flexibility revealed by high resolution crystal structures of GluK1 competitive antagonists.
Authors: Alushin, G.M. / Jane, D. / Mayer, M.L.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 22, 2012Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 1
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9938
Polymers58,4232
Non-polymers1,5706
Water6,593366
1
A: Glutamate receptor, ionotropic kainate 1
hetero molecules

A: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9938
Polymers58,4232
Non-polymers1,5706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2250 Å2
MethodPISA
2
B: Glutamate receptor, ionotropic kainate 1
hetero molecules

B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9938
Polymers58,4232
Non-polymers1,5706
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area2780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.823, 97.816, 129.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-501-

CL

21B-502-

CL

31A-767-

HOH

DetailsThe symmetry operator to build the biological dimer for chain A is x,-y,-z

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Components

#1: Protein Glutamate receptor, ionotropic kainate 1 / Glutamate receptor 5 / GluR-5 / GluR5


Mass: 29211.531 Da / Num. of mol.: 2 / Mutation: E258S
Source method: isolated from a genetically manipulated source
Details: Residues 1-2 are a cloning artefact. Residues 3-116 and 119-258 correspond to P 22756 residues 446-559 and 682-821, and are linked by residues 117-118. Residue 258 is engineered.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET 22b (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB (DE3) / References: UniProt: P22756
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-UB1 / 3-({3-[(2S)-2-amino-2-carboxyethyl]-5-methyl-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)-4,5-dibromothiophene-2-carboxylic acid


Mass: 511.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13Br2N3O6S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 18% PEG 1K, 100 mM Tris-Cl, 2.5 mM UBP315, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2006
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 57347 / Num. obs: 57347 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 27.42 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.73 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2F34

2f34


Resolution: 1.8→21.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.598 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21916 2884 5 %RANDOM
Rwork0.19756 ---
all0.19864 54463 --
obs0.19864 54463 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.393 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 86 366 4466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224348
X-RAY DIFFRACTIONr_angle_refined_deg1.3311.9965881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2615537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.3724.365181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73815819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7541524
X-RAY DIFFRACTIONr_chiral_restr0.0790.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023234
X-RAY DIFFRACTIONr_nbd_refined0.1860.22107
X-RAY DIFFRACTIONr_nbtor_refined0.2970.23079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2394
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.249
X-RAY DIFFRACTIONr_mcbond_it0.5231.52695
X-RAY DIFFRACTIONr_mcangle_it0.86724230
X-RAY DIFFRACTIONr_scbond_it1.29431950
X-RAY DIFFRACTIONr_scangle_it1.94.51651
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 223 -
Rwork0.24 3937 -
obs--99.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.88480.54430.5161.55731.13462.5850.1615-0.0014-0.12430.18970.1122-0.17030.39630.2193-0.27370.0835-0.0039-0.04140.0619-0.02320.0427-12.11662.194315.7107
21.08970.41760.36421.20411.46852.61890.2614-0.2231-0.41680.40930.4143-0.63420.65490.8544-0.67570.03920.1485-0.19940.1508-0.14840.1650.3405-3.640511.461
31.57350.54-1.14160.8265-0.48582.51130.11430.1750.16580.0040.15080.1116-0.2074-0.3652-0.26510.0579-0.00880.02140.08070.03780.0415-46.2553-12.279316.3905
41.22740.3357-1.42221.1109-0.47242.80340.42040.38130.6195-0.18230.25590.4239-0.8657-0.6385-0.67630.13880.14020.15460.03280.18640.1655-52.07060.072320.8785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1274 - 127
2X-RAY DIFFRACTION2AA128 - 254128 - 254
3X-RAY DIFFRACTION3BB4 - 1274 - 127
4X-RAY DIFFRACTION4BB128 - 254128 - 254

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