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

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Basic information

Entry
Database: PDB / ID: 5mfv
TitleCrystal structure of the GluK1 ligand-binding domain in complex with kainate and BPAM-521 at 2.18 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


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
Chem-5PX / 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: 2.181 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

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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)59,59912
Polymers58,2172
Non-polymers1,38210
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-64 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.777, 68.777, 232.891
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 A 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, 334 molecules

#2: Chemical ChemComp-5PX / 4-Cyclopropyl-3,4-dihydro-7-hydroxy-2H-1,2,4-benzothiadiazine 1,1-dioxide / BPAM-521


Mass: 240.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O3S
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 1 / 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.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 16 % PEG4000, 0.2 M lithium-sulfate, 0.1 M phosphate-citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97879 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
ReflectionResolution: 2.181→47.606 Å / Num. obs: 29453 / % possible obs: 97.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 27.92 Å2 / Rsym value: 0.074 / Net I/av σ(I): 7.146 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.181-2.32.50.1524.6187.6
2.3-2.445.60.1484.81100
2.44-2.616.50.1245.6199.9
2.61-2.826.50.1046.6199.9
2.82-3.086.50.0897.4199.7
3.08-3.456.50.0778.2199.7
3.45-3.986.40.0689.3199.4
3.98-4.886.40.06110.2199.1
4.88-6.96.20.05810198.8
6.9-47.6065.60.0510.8197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.11 Å47.61 Å
Translation5.11 Å47.61 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2refinement
SCALA3.3.20data scaling
PHASER2.5.1phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4E0X

4e0x


Resolution: 2.181→47.606 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 1497 5.09 %Random selection
Rwork0.1665 ---
obs0.1689 29430 97.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.77 Å2 / Biso mean: 29.89 Å2 / Biso min: 10.18 Å2
Refinement stepCycle: final / Resolution: 2.181→47.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3996 0 88 324 4408
Biso mean--28.2 30.33 -
Num. residues----501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084204
X-RAY DIFFRACTIONf_angle_d1.0455685
X-RAY DIFFRACTIONf_chiral_restr0.067625
X-RAY DIFFRACTIONf_plane_restr0.005709
X-RAY DIFFRACTIONf_dihedral_angle_d13.5611588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1811-2.25150.26171190.19251994211379
2.2515-2.3320.26021480.180725252673100
2.332-2.42540.25251270.17625592686100
2.4254-2.53580.28681190.172425692688100
2.5358-2.66940.2451480.177325462694100
2.6694-2.83670.24241570.183225532710100
2.8367-3.05570.2621370.184525712708100
3.0557-3.36310.22691260.18092606273299
3.3631-3.84960.20981320.15632613274599
3.8496-4.84930.1731530.13712615276898
4.8493-47.61710.15271310.16282782291397
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)
12.0709-0.3401-1.36984.0898-1.56942.83150.0797-0.00460.0598-0.6247-0.07540.4751-0.4112-0.49540.0030.3150.0154-0.09810.2460.00080.229330.72613.563-17.024
22.59460.36640.45931.4424-2.3475.2717-0.01830.00660.3037-0.3312-0.07790.3917-0.7327-0.50750.09420.34430.0954-0.06320.1721-0.02420.276329.215219.3379-12.7653
32.8118-0.1748-0.00252.9156-1.16174.1094-0.00020.00890.0239-0.2022-0.0936-0.1756-0.12220.28760.07070.1654-0.0698-0.01470.15640.00030.136943.44526.2183-12.6657
46.5330.9976-0.0264.1725-0.11042.17060.14980.0936-0.660.2104-0.0354-0.09510.4812-0.152-0.11330.2298-0.0658-0.09330.21730.01330.228126.6977-18.1897-14.0888
56.1326-0.2626-2.10348.31570.06438.52060.080.4152-0.6423-0.0554-0.0199-0.62730.37170.0258-0.08270.13660.0167-0.03240.20820.00990.33640.2141-14.9864-14.4757
61.83961.86690.54712.72171.43511.96480.02880.11610.11690.0282-0.06360.15150.0478-0.18520.03140.17920.0018-0.00680.23470.05610.190428.0775-5.7151-14.8228
77.18611.4306-0.12213.38420.40483.4790.0285-0.22130.42240.0393-0.14060.2366-0.5537-0.15450.09060.26990.0213-0.03420.11950.00290.171233.028412.87031.2372
81.34211.3592.6687.58322.3275.32510.194-0.02720.44810.3824-0.07651.56540.0975-1.3155-0.12790.17040.0541-0.020.39810.02430.482418.74336.8173-8.4559
96.1469-2.46050.63291.33310.24242.5927-0.1904-0.0893-0.0617-0.03110.30880.29590.5846-0.1205-0.10850.3142-0.0556-0.06120.14940.01540.115644.4645-7.13721.3632
102.7787-0.47560.71892.3659-2.91658.23320.0517-0.0413-0.1546-0.0526-0.0748-0.30630.43270.55230.09420.22670.0433-0.05530.17840.01150.225651.0918-9.80817.9514
111.5624-0.51170.35542.4221-0.4183.17870.0713-0.120.07280.26130.0111-0.0635-0.25230.2064-0.05580.2224-0.0949-0.01680.1745-0.00430.198342.08586.97616.5153
124.5791.6774-0.62676.0654-0.68063.23950.17210.02780.51110.2011-0.04720.6096-0.1-0.7779-0.06860.217-0.02740.00260.3387-0.01860.226318.2121.558418.3413
135.6492-1.07020.1837.13380.98395.9390.06090.21690.41850.448-0.09890.6459-0.4605-0.53520.03870.22740.01610.06650.25760.01260.241620.25757.764322.1023
142.97581.6166-1.40541.2235-0.68491.66360.0505-0.0713-0.04280.1373-0.1609-0.04730.0253-0.1450.10160.2397-0.0484-0.05260.19630.00410.172729.0605-4.499216.7687
156.39142.13530.52394.1350.88825.78410.11030.1227-0.4258-0.1011-0.138-0.29520.3302-0.08710.0370.13620.0182-0.020.120.04150.185244.9126-7.07841.939
163.24980.8708-3.41931.4577-0.18474.0336-0.58770.3184-0.74390.21190.07330.10410.6684-0.45560.3320.3839-0.1037-0.05610.19110.01550.370732.7572-17.441913.2972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 432:450)A432 - 450
2X-RAY DIFFRACTION2(chain A and resid 451:479)A451 - 479
3X-RAY DIFFRACTION3(chain A and resid 480:537)A480 - 537
4X-RAY DIFFRACTION4(chain A and resid 538:685)A538 - 685
5X-RAY DIFFRACTION5(chain A and resid 686:713)A686 - 713
6X-RAY DIFFRACTION6(chain A and resid 714:770)A714 - 770
7X-RAY DIFFRACTION7(chain A and resid 771:795)A771 - 795
8X-RAY DIFFRACTION8(chain A and resid 796:801)A796 - 801
9X-RAY DIFFRACTION9(chain B and resid 433:449)B433 - 449
10X-RAY DIFFRACTION10(chain B and resid 450:482)B450 - 482
11X-RAY DIFFRACTION11(chain B and resid 483:536)B483 - 536
12X-RAY DIFFRACTION12(chain B and resid 537:697)B537 - 697
13X-RAY DIFFRACTION13(chain B and resid 698:722)B698 - 722
14X-RAY DIFFRACTION14(chain B and resid 723:775)B723 - 775
15X-RAY DIFFRACTION15(chain B and resid 776:794)B776 - 794
16X-RAY DIFFRACTION16(chain B and resid 795:805)B795 - 805

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