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- PDB-3c35: Crystal structure of GluR5 ligand-binding core in complex with ce... -

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Basic information

Entry
Database: PDB / ID: 3c35
TitleCrystal structure of GluR5 ligand-binding core in complex with cesium at 1.97 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 / 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
: / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.97 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

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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)60,97321
Polymers58,5072
Non-polymers2,46619
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-9 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.587, 70.587, 234.359
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, 419 molecules

#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / 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 / Comment: neurotransmitter, agonist*YM
#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.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 4000, 125 mM CsCl, 175 mM Cs2(SO4), 100 mM Cs 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: Dec 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: 1.97→30 Å / Num. all: 43097 / Num. obs: 43097 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.9
Reflection shellResolution: 1.97→2.05 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.7 / % possible all: 98.8

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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: 1.97→29.27 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.68 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22735 2156 5.1 %RANDOM
Rwork0.17943 ---
all0.18194 39746 --
obs0.18194 39746 97.43 %-
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: 19.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2--0.82 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.97→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 62 400 4510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224180
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9865636
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47224.237177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10615780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1661524
X-RAY DIFFRACTIONr_chiral_restr0.1140.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213058
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_it0.8461.52529
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60524090
X-RAY DIFFRACTIONr_scbond_it2.69131651
X-RAY DIFFRACTIONr_scangle_it4.3044.51545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 156 -
Rwork0.199 2887 -
obs--97.47 %
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)
11.6196-0.0097-0.46510.8437-0.05891.8388-0.04540.0570.0461-0.05870.0344-0.05680.00650.09130.01110.05610.02110.00550.01670.00430.047510.76128.61944.513
21.18130.23440.2252.17020.14121.7426-0.0445-0.0279-0.028-0.12910.03340.0961-0.1592-0.28560.01110.05090.06310.01410.02170.00910.0057-11.34739.68744.036
31.59190.5262-0.08361.8893-0.39592.39220.0745-0.12370.1522-0.0148-0.0619-0.0849-0.0870.2074-0.01270.04080.00870.01720.0498-0.00090.048210.81435.68955.36
41.29470.3968-0.64110.8307-0.37632.89690.0008-0.1716-0.02990.0037-0.04-0.02020.24350.11120.03910.0330.0317-0.00910.04780.0140.0302-1.27723.47576.964
52.7224-0.77940.95381.66510.01452.1496-0.03680.07960.2274-0.0041-0.004-0.1428-0.16270.16620.0409-0.0031-0.02240.00990.0260.02470.04513.82247.99378.047
62.1392-0.020.09420.820.27862.1598-0.0269-0.01820.012-0.05580.03490.08590.0919-0.0646-0.0080.0560.01710.00620.05490.0290.0367-5.82328.27766.142
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1065 - 106
2X-RAY DIFFRACTION2AA107 - 213107 - 213
3X-RAY DIFFRACTION3AA214 - 257214 - 257
4X-RAY DIFFRACTION4BB5 - 1085 - 108
5X-RAY DIFFRACTION5BB109 - 210109 - 210
6X-RAY DIFFRACTION6BB211 - 257211 - 257

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