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- PDB-2f35: Crystal Structure of the GluR5 Ligand Binding Core with UBP302 At... -

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Entry
Database: PDB / ID: 2f35
TitleCrystal Structure of the GluR5 Ligand Binding Core with UBP302 At 1.87 Angstroms 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
Chem-UBC / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.87 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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: 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)59,6378
Polymers58,4232
Non-polymers1,2146
Water7,494416
1
A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8194
Polymers29,2121
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8194
Polymers29,2121
Non-polymers6073
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)59,6378
Polymers58,4232
Non-polymers1,2146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2160 Å2
ΔGint-24 kcal/mol
Surface area24060 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)59,6378
Polymers58,4232
Non-polymers1,2146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area2690 Å2
ΔGint-26 kcal/mol
Surface area24310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.876, 97.907, 128.347
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-803-

HOH

41B-837-

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


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-UBC / (S)-1-(2-AMINO-2-CARBOXYETHYL)-3-(2-CARBOXYBENZYL)PYRIMIDINE-2,4-DIONE


Mass: 333.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N3O6 / Comment: antagonist*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 20% PEG 1K 100 mM Tris 5 mM UBP302, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 28, 2005 / Details: Confocal mirrors
RadiationMonochromator: Multilayer confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→40 Å / Num. all: 52211 / Num. obs: 52211 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 28.08 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.3
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.43 / % possible all: 85.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: in process UBP310

Resolution: 1.87→38.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.227 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22036 2595 5.1 %RANDOM
Rwork0.19125 ---
all0.19273 48777 --
obs0.19273 48777 99.8 %-
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: 18.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.87→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4014 0 82 416 4512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224497
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9926086
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5425563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.3524.611193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.93115861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9731525
X-RAY DIFFRACTIONr_chiral_restr0.1140.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023383
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2420.32437
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.53194
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.5747
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.3118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2880.584
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.03422796
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55434398
X-RAY DIFFRACTIONr_scbond_it1.16121984
X-RAY DIFFRACTIONr_scangle_it1.57431688
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.866→1.915 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 205 -
Rwork0.275 3476 -
obs--97.43 %
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)
10.6620.74510.87491.00511.40942.23990.0277-0.0039-0.090.02520.1963-0.009-0.11310.2468-0.2240.0821-0.04820.01780.1086-0.04990.0759-7.560413.758219.4207
21.4629-0.0165-0.10532.35580.95972.51190.1042-0.03660.03310.0712-0.04980.02940.0992-0.03-0.05440.0285-0.0298-0.0187-0.00090.00630.0125-19.8090.65298.1692
310.20320.9081-2.91580.67630.55431.94560.78141.33452.3520.0249-0.7051-0.48580.3365-0.3142-0.07630.631-0.2207-0.01570.0722-0.03420.0694-43.4036-2.938717.3561
41.64330.67860.09311.81450.89732.7360.14040.04470.1836-0.0761-0.07690.0647-0.0412-0.2028-0.06350.0815-0.00530.00340.0075-0.0010.0178-22.41965.52143.9937
50.9710.7722-1.35810.7152-0.87492.31620.2022-0.0016-0.00320.01340.0220.0973-0.28140.1431-0.22420.1197-0.05260.05340.0776-0.0190.068-34.0204-6.616612.2112
62.3211-0.1201-0.93091.54080.21022.5741-0.06040.0728-0.0366-0.02370.1128-0.04090.0418-0.0886-0.05240.0034-0.0309-0.00420.01820.01670.0122-48.0659-20.164824.1318
72.88150.4084-0.35237.9510.9680.93560.10410.5369-0.57680.5837-0.07910.3066-0.1599-0.5889-0.0250.0462-0.1625-0.02820.5537-0.08380.2498-58.5241-27.542822.8741
81.81480.6671-0.86631.6087-0.10732.8694-0.0621-0.0416-0.04840.02540.1357-0.15280.2111-0.0174-0.07370.0117-0.01150.00240.06320.00020.0156-44.2225-21.931227.1404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 714 - 71
2X-RAY DIFFRACTION2AA72 - 11972 - 119
3X-RAY DIFFRACTION3AA120 - 181120 - 181
4X-RAY DIFFRACTION4AA182 - 254182 - 254
5X-RAY DIFFRACTION5BB4 - 714 - 71
6X-RAY DIFFRACTION6BB72 - 11972 - 119
7X-RAY DIFFRACTION7BB120 - 188120 - 188
8X-RAY DIFFRACTION8BB189 - 254189 - 254

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