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- PDB-5mfw: Crystal structure of the GluK1 ligand-binding domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 5mfw
TitleCrystal structure of the GluK1 ligand-binding domain in complex with kainate and BPAM-121 at 2.10 A resolution
ComponentsGlutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor / GluK1 ligand-binding domain / positive allosteric modulator
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 / 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 / glutamate binding ...negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate binding / inhibitory postsynaptic potential / synaptic transmission, GABAergic / adult behavior / behavioral response to pain / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / membrane depolarization / glutamate-gated receptor activity / glutamate-gated calcium ion channel 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 / SNARE binding / positive regulation of synaptic transmission, GABAergic / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / establishment of localization in cell / postsynaptic density membrane / regulation of synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / nervous system development / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / receptor complex / postsynaptic density / neuronal cell body / synapse / dendrite / 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-7M6 / ACETATE ION / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLarsen, A.P. / Frydenvang, K. / Kastrup, J.S.
Citation
Journal: Mol. Pharmacol. / Year: 2017
Title: Identification and Structure-Function Study of Positive Allosteric Modulators of Kainate Receptors.
Authors: Larsen, A.P. / Fievre, S. / Frydenvang, K. / Francotte, P. / Pirotte, B. / Kastrup, J.S. / Mulle, C.
#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
DepositionNov 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,93215
Polymers58,2172
Non-polymers1,71513
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-64 kcal/mol
Surface area22890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.644, 68.644, 234.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 ionotropic, kainate 1 / GluK1 / Glutamate receptor 5 / GluR5


Mass: 29108.453 Da / Num. of mol.: 2 / Fragment: UNP residues 445-559,UNP residues 682-820
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 545 AND 546 OF THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 545 AND 546 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (430-544, 667-805). RESIDUE 429 IS REMNANT FROM CLONING.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Variant (production host): ORIGAMI 2 / References: UniProt: P22756

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Non-polymers , 7 types, 489 molecules

#2: Chemical ChemComp-7M6 / 7-chloro-4-(2-fluoroethyl)-2,3-dihydro-1,2,4-benzothiadiazine 1,1-dioxide


Mass: 264.704 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10ClFN2O2S
#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
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE DATABASE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR ...THE SEQUENCE DATABASE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER.THERE IS A SEQUENCE CONFLICT AT RESIDUE 462 OF THE CRYSTALLIZED PROTEIN DUE TO DIFFERENCES IN DATABASE SEQUENCE (SEE GENBANK ACCESION NO.AAA02874).

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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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 % PEG4000, 0.3 M lithium-sulfate, 0.1 M sodium-acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→29.631 Å / Num. obs: 33935 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 22.17 Å2 / Rsym value: 0.089 / Net I/av σ(I): 6.975 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.217.10.3722199.6
2.21-2.358.50.2972.41100
2.35-2.518.50.2233.31100
2.51-2.718.50.1594.71100
2.71-2.978.50.1056.81100
2.97-3.328.40.0729.61100
3.32-3.838.40.05511.61100
3.83-4.78.20.04712.21100
4.7-6.6480.049111100
6.64-29.6317.20.04610.1198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.66 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.63 Å
Translation2.5 Å29.63 Å

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Processing

Software
NameVersionClassification
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIX1.8.2refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E0X

4e0x


Resolution: 2.1→29.631 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.61
RfactorNum. reflection% reflectionSelection details
Rfree0.2185 1717 5.08 %Random selection
Rwork0.1629 ---
obs0.1657 33831 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.2 Å2 / Biso mean: 18.44 Å2 / Biso min: 2.42 Å2
Refinement stepCycle: final / Resolution: 2.1→29.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4006 0 104 476 4586
Biso mean--25.18 23.05 -
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064217
X-RAY DIFFRACTIONf_angle_d1.0085705
X-RAY DIFFRACTIONf_chiral_restr0.067628
X-RAY DIFFRACTIONf_plane_restr0.005710
X-RAY DIFFRACTIONf_dihedral_angle_d13.3441617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.16180.24311430.17852589273299
2.1618-2.23150.24791400.174926062746100
2.2315-2.31130.26831380.176726382776100
2.3113-2.40380.24191170.173226422759100
2.4038-2.51310.22861630.176826032766100
2.5131-2.64550.26361860.175826242810100
2.6455-2.81120.24751220.176326472769100
2.8112-3.0280.23961400.182126742814100
3.028-3.33240.21481370.172326962833100
3.3324-3.81370.21681500.147427072857100
3.8137-4.80150.16491430.13127472890100
4.8015-29.63360.18211380.161629413079100

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