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- PDB-2f34: Crystal Structure of the GluR5 Ligand Binding Core Dimer with UBP... -

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Entry
Database: PDB / ID: 2f34
TitleCrystal Structure of the GluR5 Ligand Binding Core Dimer with UBP310 At 1.74 Angstroms Resolution
ComponentsGLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / 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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential ...gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / 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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / modulation of excitatory postsynaptic potential / behavioral response to pain / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / sodium ion transmembrane transport / glutamate-gated receptor activity / potassium ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / excitatory postsynaptic potential / presynaptic modulation of chemical synaptic transmission / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / regulation of synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / nervous system development / chemical synaptic transmission / scaffold protein binding / postsynaptic density / receptor complex / neuronal cell body / dendrite / glutamatergic synapse / synapse / membrane / identical protein binding / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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 / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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-UBA / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMayer, M.L.
Citation
Journal: J.Neurosci. / Year: 2006
Title: Crystal structures of the kainate receptor GluR5 ligand binding core dimer with novel GluR5-selective antagonists.
Authors: Mayer, M.L. / Ghosal, A. / Dolman, N.P. / Jane, D.E.
#1: 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
DepositionNov 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 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 1.5Aug 23, 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)59,6778
Polymers58,4232
Non-polymers1,2546
Water8,683482
1
A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8394
Polymers29,2121
Non-polymers6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8394
Polymers29,2121
Non-polymers6273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
hetero molecules

A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6778
Polymers58,4232
Non-polymers1,2546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2200 Å2
ΔGint-25 kcal/mol
Surface area23750 Å2
MethodPISA, PQS
4
B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
hetero molecules

B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6778
Polymers58,4232
Non-polymers1,2546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area2740 Å2
ΔGint-27 kcal/mol
Surface area24230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.698, 97.954, 129.126
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-1031-

HOH

41B-1036-

HOH

DetailsThe chain A dimer is generated by the two-fold axis: 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
Fragment: GluR5 ligand binding core (sequence database 446-559 and 682-821)
Mutation: E791S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1 / Plasmid: PET22 (MODIFIED) / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B (DE3) / References: UniProt: P22756
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-UBA / (S)-1-(2-AMINO-2-CARBOXYETHYL)-3(2-CARBOXYTHIOPHENE-3-YL-METHYL)-5-METHYLPYRIMIDINE-2,4-DIONE


Mass: 353.350 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N3O6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 17-22% PEG 1K 100mM TRIS 5mM UBP310, pH 8.6, 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: MARRESEARCH / Detector: CCD / Date: Aug 11, 2005
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: 1.74→40 Å / Num. all: 64151 / Num. obs: 64151 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 25.16 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 14.5
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.38 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TXF

1txf


Resolution: 1.74→33.41 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.895 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21135 3218 5.1 %RANDOM
Rwork0.18103 ---
all0.18255 60378 --
obs0.18255 60378 99.92 %-
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: 19.284 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.74→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 82 482 4578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224547
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9936166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7625576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.87924.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.62615877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2031527
X-RAY DIFFRACTIONr_chiral_restr0.1240.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023425
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.32423
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.53299
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.5821
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.3101
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.5100
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.12322811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71834469
X-RAY DIFFRACTIONr_scbond_it1.3322008
X-RAY DIFFRACTIONr_scangle_it1.87631697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 265 -
Rwork0.21 4373 -
obs--99.76 %
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)
10.37750.70590.99991.4491.64463.04110.0985-0.0309-0.0430.08130.1615-0.0743-0.05070.2934-0.26010.0627-0.0720.01330.1094-0.0620.0827-7.58113.50820.866
21.81960.3076-0.05222.4351.34252.71580.1982-0.05280.09430.1226-0.05790.00130.1522-0.0835-0.14030.0162-0.0494-0.0112-0.00290.01380.0173-18.92.5979.665
31.5248-0.03970.54113.31251.09762.67120.01990.12050.1052-0.6743-0.05870.5608-0.3116-0.52040.03880.238-0.07350.15830.38570.00510.16-25.10510.852-11.4
41.38450.54220.2991.76391.48353.6080.2019-0.07530.04980.089-0.0769-0.04810.1022-0.1436-0.1250.0207-0.0315-0.0174-0.00830.00210.0166-19.3852.2097.749
51.38530.7122-1.59540.3921-0.99613.02840.17690.04410.0661-0.02540.07720.052-0.30490.1112-0.25410.1112-0.07480.06260.0618-0.01750.0734-34.841-7.17912.097
62.40380.1888-1.29981.8043-0.0512.7508-0.0680.1134-0.0179-0.06930.1941-0.08480.074-0.153-0.1261-0.0031-0.0495-0.0130.01730.01070.0175-46.504-18.68522.455
73.3621-0.5875-0.95041.82840.29982.8606-0.2017-0.9314-0.68560.57580.40660.19120.67790.2063-0.2050.32930.0087-0.09140.13560.01250.113-38.113-29.04447.729
81.79270.4731-1.24081.5021-0.11343.531-0.06520.05860.0262-0.06510.1749-0.05840.1229-0.1072-0.1097-0.009-0.0330.00270.01980.01780.01-46.557-19.4324.606
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 694 - 69
2X-RAY DIFFRACTION2AA70 - 12770 - 127
3X-RAY DIFFRACTION3AA128 - 213128 - 213
4X-RAY DIFFRACTION4AA214 - 254214 - 254
5X-RAY DIFFRACTION5BB4 - 694 - 69
6X-RAY DIFFRACTION6BB70 - 12770 - 127
7X-RAY DIFFRACTION7BB128 - 213128 - 213
8X-RAY DIFFRACTION8BB214 - 254214 - 254

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