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- PDB-3c36: Crystal structure of GluR5 ligand-binding core in complex with am... -

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Basic information

Entry
Database: PDB / ID: 3c36
TitleCrystal structure of GluR5 ligand-binding core in complex with ammonium ions at 1.68 Angstrom resolution
ComponentsGLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate binding ...negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate binding / inhibitory postsynaptic potential / synaptic transmission, GABAergic / adult behavior / behavioral response to pain / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / membrane depolarization / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / SNARE binding / positive regulation of synaptic transmission, GABAergic / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / nervous system development / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / receptor complex / postsynaptic density / neuronal cell body / synapse / dendrite / glutamatergic 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
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / AMMONIUM ION / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.68 Å
AuthorsMayer, M.L.
Citation
Journal: Neuron / Year: 2008
Title: Molecular basis of kainate receptor modulation by sodium.
Authors: Plested, A.J. / Vijayan, R. / Biggin, P.C. / Mayer, M.L.
#1: Journal: Neuron / Year: 2007
Title: Structure and mechanism of kainate receptor modulation by anions
Authors: Plested, A.J. / Mayer, M.L.
#2: Journal: Neuron / Year: 2005
Title: Crystal structures of the GluR5 and GluR6 ligand binding cores: molecular mechanisms underlying kainate receptor selectivity
Authors: Mayer, M.L.
History
DepositionJan 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)59,38813
Polymers58,5072
Non-polymers88111
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-8.4 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.760, 70.760, 234.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1 / Glutamate receptor 5 / GluR-5 / GluR5


Mass: 29253.566 Da / Num. of mol.: 2 / Fragment: Residues 446-821
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK1, GLUR5 / Plasmid: Modified pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE3) / References: UniProt: P22756

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Non-polymers , 5 types, 549 molecules

#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE


Mass: 213.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15NO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE FIRST TWO RESIDUES OF THE SEQUENCE ARE VECTOR ENCODED. GLUR5 RESIDUES 446-559 AND 682-821 ARE ...THE FIRST TWO RESIDUES OF THE SEQUENCE ARE VECTOR ENCODED. GLUR5 RESIDUES 446-559 AND 682-821 ARE LINKED VIA GLY-THR DIPEPTIDE.

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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: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 4000, 125 mM NH4Cl, 175 mM (NH4)2(SO4), 100 mM NH4 cacodylate, 4 mM Kainic acid, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2007
RadiationMonochromator: DOUBLE CRYSTAL SI-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→40 Å / Num. all: 68619 / Num. obs: 68619 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.3
Reflection shellResolution: 1.68→1.76 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 4.5 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3C31

3c31


Resolution: 1.68→39.07 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.323 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2006 3453 5.1 %RANDOM
Rwork0.16683 ---
all0.16858 64816 --
obs0.16858 64816 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.335 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.68→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 54 538 4640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224411
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7651.9835989
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62224.439187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15915823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1881525
X-RAY DIFFRACTIONr_chiral_restr0.1410.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213311
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0491.52688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86824385
X-RAY DIFFRACTIONr_scbond_it3.13531723
X-RAY DIFFRACTIONr_scangle_it4.9814.51603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.727 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 241 -
Rwork0.19 4592 -
obs--97.07 %
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)
11.5514-0.0172-0.36210.71160.06221.5498-0.02910.03910.0389-0.07730.0264-0.05630.02840.12610.00270.06110.02940.00850.0250.01130.041910.47628.86344.846
21.1652-0.2457-0.00332.6782-0.4411.4866-0.00370.0006-0.0301-0.05320.06290.2988-0.0824-0.3718-0.05920.0360.063-0.00190.05670.01990.0187-15.95437.55445.186
31.0744-0.73150.47640.8377-0.36781.2642-0.0429-0.06580.0441-0.11660.0347-0.064-0.114-0.09010.00830.10550.03130.0176-0.00430.00520.0348-4.76740.33943.57
40.90020.6138-0.04162.7124-0.74762.85710.0178-0.14350.1769-0.0349-0.0152-0.0118-0.16010.222-0.00260.00780.00490.01830.0729-0.00510.058311.74638.16156.049
51.08570.3495-0.52460.8549-0.39312.21770.0066-0.162-0.0065-0.0203-0.0503-0.00410.19790.10080.04380.01730.0385-0.00470.08460.01170.0217-1.38923.46876.811
62.3289-0.94250.39312.4859-0.10052.64530.0210.12030.30230.0168-0.0711-0.2383-0.34590.42740.0502-0.0261-0.08280.00470.09410.03130.04248.64749.61276.299
70.2599-0.19940.05891.44640.2851.0049-0.0012-0.01520.0231-0.0221-0.01680.0627-0.10690.07250.01790.00380.00590.00990.08340.02230.0524-0.85741.94777.492
81.9169-1.119-0.6641.77691.23343.5665-0.0191-0.06670.0309-0.0673-0.00230.0958-0.0119-0.20720.02140.02680.0072-0.00620.07020.02440.053-10.04328.82965.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1085 - 108
2X-RAY DIFFRACTION2AA109 - 164109 - 164
3X-RAY DIFFRACTION3AA165 - 223165 - 223
4X-RAY DIFFRACTION4AA224 - 257224 - 257
5X-RAY DIFFRACTION5BB5 - 1085 - 108
6X-RAY DIFFRACTION6BB109 - 164109 - 164
7X-RAY DIFFRACTION7BB165 - 225165 - 225
8X-RAY DIFFRACTION8BB226 - 257226 - 257

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