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- PDB-3c31: Crystal structure of GluR5 ligand-binding core in complex with li... -

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Basic information

Entry
Database: PDB / ID: 3c31
TitleCrystal structure of GluR5 ligand-binding core in complex with lithium at 1.49 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 / amino acid transmembrane transport / 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 ...negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / amino acid transmembrane transport / 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 / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / modulation of excitatory postsynaptic potential / behavioral response to pain / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / membrane depolarization / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / potassium ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / excitatory postsynaptic potential / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / establishment of localization in cell / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / regulation of synaptic plasticity / presynaptic membrane / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / receptor complex / postsynaptic density / neuronal cell body / dendrite / synapse / 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 / : / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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 1.3Aug 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_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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)59,55415
Polymers58,5072
Non-polymers1,04713
Water12,430690
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-9.3 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.529, 70.529, 234.128
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 , 6 types, 703 molecules

#2: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#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 / Comment: neurotransmitter, agonist*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 4000, 125 mM LiCl, 175 mM Li2(SO4), 100 mM Li 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: Aug 19, 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: 1.49→35 Å / Num. all: 97909 / Num. obs: 97909 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 16.17 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.5
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 3.9 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TT1

1tt1


Resolution: 1.49→34.88 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.867 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19024 4817 5.1 %RANDOM
Rwork0.16527 ---
all0.16655 90487 --
obs0.16655 90487 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.038 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.49→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4048 0 65 690 4803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224508
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9936155
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8485601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64924.694196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29215870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6411525
X-RAY DIFFRACTIONr_chiral_restr0.1270.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023355
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.22226
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.23193
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2565
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1450.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.255
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1551.52760
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.724425
X-RAY DIFFRACTIONr_scbond_it2.75431973
X-RAY DIFFRACTIONr_scangle_it4.1564.51684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 321 -
Rwork0.2 6131 -
obs--91.08 %
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)
11.41350.0519-0.15630.68440.02361.1986-0.00420.1410.0738-0.06680.0043-0.06680.01860.0951-0.00010.03050.01650.00810.03670.02110.025610.27828.80144.685
20.8699-0.06270.16131.1533-0.49261.1143-0.0255-0.0407-0.03680.00430.06160.0675-0.0368-0.1261-0.0360.02460.02370.00890.02780.01190.0271-11.88839.88943.869
31.0590.17560.17711.2748-0.00441.40090.0186-0.00470.1545-0.0041-0.0206-0.0312-0.0840.09580.0020.0260.00210.01460.05070.01450.05510.55935.51755.464
40.61330.054-0.26380.5256-0.08020.9859-0.00370.00660.00550.03350.00620.01110.0537-0.0514-0.00240.02510.0094-0.00210.03960.010.0269-1.92723.19476.85
51.5026-0.30490.13621.07520.47931.67060.017-0.08620.0665-0.02550.0146-0.0991-0.25580.1336-0.03170.0316-0.02490.00480.01370.02340.01713.89547.37777.635
61.4514-0.2120.41940.8844-0.00281.4736-0.0175-0.01220.056-0.02570.02060.1119-0.0666-0.1172-0.00320.04160.00570.00480.06450.0280.0505-7.30427.69565.95
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1075 - 107
2X-RAY DIFFRACTION2AA108 - 213108 - 213
3X-RAY DIFFRACTION3AA214 - 257214 - 257
4X-RAY DIFFRACTION4BB5 - 1075 - 107
5X-RAY DIFFRACTION5BB108 - 213108 - 213
6X-RAY DIFFRACTION6BB214 - 257214 - 257

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