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- PDB-4e0x: Crystal structure of the kainate receptor GluK1 ligand-binding do... -

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Basic information

Entry
Database: PDB / ID: 4e0x
TitleCrystal structure of the kainate receptor GluK1 ligand-binding domain in complex with kainate in the absence of glycerol
ComponentsGlutamate receptor, ionotropic kainate 1
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor / GluK1 / ligand-binding domain / agonist
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 / behavioral response to pain / modulation of excitatory postsynaptic potential / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor 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 / excitatory postsynaptic potential / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / 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 density / receptor complex / neuronal cell body / glutamatergic synapse / synapse / dendrite / identical protein binding / membrane / 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
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFrydenvang, K. / Kastrup, J.S.
Citation
Journal: Neurochem Int / Year: 2012
Title: Kainate induces various domain closures in AMPA and kainate receptors.
Authors: Venskutonyte, R. / Frydenvang, K. / Hald, H. / Rabassa, A.C. / Gajhede, M. / Ahring, P.K. / Kastrup, J.S.
#1: Journal: FEBS Lett. / Year: 2005
Title: Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate
Authors: Naur, P. / Vestergaard, B. / Skov, L.K. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S.
History
DepositionMar 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 13, 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

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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)59,32613
Polymers58,2172
Non-polymers1,10911
Water8,179454
1
A: Glutamate receptor, ionotropic kainate 1
B: Glutamate receptor, ionotropic kainate 1
hetero molecules

A: Glutamate receptor, ionotropic kainate 1
B: Glutamate receptor, ionotropic kainate 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,65226
Polymers116,4344
Non-polymers2,21822
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7190 Å2
ΔGint-175 kcal/mol
Surface area45680 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-90 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.256, 68.256, 235.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsA complete tetrameric multimer representing the known biologically significant oligomerization state of the molecule cannot be generated by symmetry within the crystal.

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Components

#1: Protein Glutamate receptor, ionotropic kainate 1 / Glutamate receptor 5 / GluR-5 / GluR5


Mass: 29108.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur5, Grik1 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756
#2: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsNATIVE GLUK1 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING ...NATIVE GLUK1 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (430-544, 667-805). GLY1 IS A CLONING REMNANCE.

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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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG4000, 0.35M lithium sulfate, 0.1M sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29.513 Å / Num. all: 38773 / Num. obs: 38773 / % possible obs: 100 % / Redundancy: 6.4 % / Rsym value: 0.072 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.116.40.4111.83546655080.411100
2.11-2.246.50.25733415752520.257100
2.24-2.396.50.1993.83199249410.199100
2.39-2.586.50.1375.63014546430.137100
2.58-2.836.50.0977.82776142950.097100
2.83-3.166.40.06112.12510338940.061100
3.16-3.656.40.04116.52213334640.041100
3.65-4.476.30.03416.61885829930.034100
4.47-6.326.20.03116.21460123740.031100
6.32-29.5135.60.02520.9783214090.02598.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C32

3c32


Resolution: 2→29.513 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8695 / SU ML: 0.51 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.55 / Stereochemistry target values: ML
Details: Residues 1-3 (GAN) in chain A and B, as well as residues 253-257 (GNGCP) in chain A could not be located in the electron density map
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 1938 5.01 %RANDOM
Rwork0.1747 ---
obs0.1769 38661 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.991 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 93.45 Å2 / Biso mean: 25.8507 Å2 / Biso min: 10.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.3598 Å20 Å2-0 Å2
2--3.3598 Å2-0 Å2
3----6.7196 Å2
Refinement stepCycle: LAST / Resolution: 2→29.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 63 454 4537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084172
X-RAY DIFFRACTIONf_angle_d1.0045637
X-RAY DIFFRACTIONf_chiral_restr0.073624
X-RAY DIFFRACTIONf_plane_restr0.005705
X-RAY DIFFRACTIONf_dihedral_angle_d14.961574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2-2.050.25721540.1978253326872533
2.05-2.10540.23811380.1965256527032565
2.1054-2.16740.25481260.193255926852559
2.1674-2.23730.24161310.1851258927202589
2.2373-2.31720.2141410.183257327142573
2.3172-2.410.24081280.1853259527232595
2.41-2.51960.25881190.1815261127302611
2.5196-2.65240.23141440.1869258027242580
2.6524-2.81840.25141420.1917261227542612
2.8184-3.03580.22361380.1967262427622624
3.0358-3.3410.23771470.1814263227792632
3.341-3.82350.2141420.1614266928112669
3.8235-4.81380.16511410.137270728482707
4.8138-29.51640.19331470.1705287430212874

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