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- PDB-4ymb: Structure of the ligand-binding domain of GluK1 in complex with t... -

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Basic information

Entry
Database: PDB / ID: 4ymb
TitleStructure of the ligand-binding domain of GluK1 in complex with the antagonist CNG10111
ComponentsGlutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1
KeywordsSIGNALING PROTEIN / Ionotropic glutamate receptor / kainate receptor GluK1 / ligand-binding domain / antagonist / fusion 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 / 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
(3R,4S)-3-(3-carboxyphenyl)-4-propyl-L-proline / ACETATE ION / DI(HYDROXYETHYL)ETHER / Glutamate receptor ionotropic, kainate 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsMoller, C. / Tapken, D. / Kastrup, J.S. / Frydenvang, K.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Denmark
Citation
Journal: J.Med.Chem. / Year: 2015
Title: Structure-Activity Relationship Study of Ionotropic Glutamate Receptor Antagonist (2S,3R)-3-(3-Carboxyphenyl)pyrrolidine-2-carboxylic Acid.
Authors: Krogsgaard-Larsen, N. / Storgaard, M. / Moller, C. / Demmer, C.S. / Hansen, J. / Han, L. / Monrad, R.N. / Nielsen, B. / Tapken, D. / Pickering, D.S. / Kastrup, J.S. / Frydenvang, K. / Bunch, L.
#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 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Database references / Category: citation_author / diffrn_source
Item: _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 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

Downloads & links

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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)59,31814
Polymers58,2172
Non-polymers1,10112
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-45 kcal/mol
Surface area24260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.813, 71.813, 230.126
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
Source method: isolated from a genetically manipulated source
Details: The protein comprises segment S1 residues 445-559, a GT linker and S2 residues 682-820
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / References: UniProt: P22756

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Non-polymers , 6 types, 500 molecules

#2: Chemical ChemComp-4E7 / (3R,4S)-3-(3-carboxyphenyl)-4-propyl-L-proline


Mass: 277.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H19NO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG8000, lithium sulfate, TRIS

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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: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→68.553 Å / Num. all: 46519 / Num. obs: 46519 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 18.82 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Rsym value: 0.071 / Net I/av σ(I): 6.073 / Net I/σ(I): 18.1 / Num. measured all: 347630
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.93-2.036.80.33824502366570.1410.3385.699.9
2.03-2.167.80.23.64885662880.0760.28.8100
2.16-2.317.40.2071.74396859560.0910.20711.3100
2.31-2.497.80.17.44322655560.0380.114.3100
2.49-2.737.80.0789.33983551210.030.07817.7100
2.73-3.057.70.05413.23619346760.0210.05422.9100
3.05-3.527.70.04414.93194041590.0170.04429.7100
3.52-4.327.40.04911.32629035730.0190.04934.7100
4.32-6.17.40.03216.92096028300.0120.03235.4100
6.1-46.4576.70.0377.61133917030.0170.03733.499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.31 Å44.9 Å
Translation2.31 Å44.9 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DLD

4dld


Resolution: 1.93→44.9 Å / FOM work R set: 0.8593 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 4353 5.06 %Random
Rwork0.179 81606 --
obs0.1811 46242 99.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.65 Å2 / Biso mean: 26.56 Å2 / Biso min: 7.34 Å2
Refinement stepCycle: final / Resolution: 1.93→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4043 0 135 489 4667
Biso mean--31.55 29.64 -
Num. residues----507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094283
X-RAY DIFFRACTIONf_angle_d1.1035789
X-RAY DIFFRACTIONf_chiral_restr0.043641
X-RAY DIFFRACTIONf_plane_restr0.005733
X-RAY DIFFRACTIONf_dihedral_angle_d13.6071639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9301-1.9520.28991690.34672613278296
1.952-1.9750.41331660.27122688285498
1.975-1.9990.2041400.207327402880100
1.999-2.02430.2321380.181127232861100
2.0243-2.0510.20811280.187227672895100
2.051-2.07910.2381490.187927222871100
2.0791-2.10880.24161310.182727722903100
2.1088-2.14030.25421320.181627212853100
2.1403-2.17370.21851430.186627902933100
2.1737-2.20930.2281320.196527142846100
2.2093-2.24740.36461490.32542518266791
2.2474-2.28830.37051570.28082587274497
2.2883-2.33230.25311370.187427632900100
2.3323-2.37990.27451370.178527322869100
2.3799-2.43170.2491470.17827352882100
2.4317-2.48820.24971600.172627222882100
2.4882-2.55040.20741440.172527642908100
2.5504-2.61940.19731430.171327112854100
2.6194-2.69650.22781490.170227262875100
2.6965-2.78350.22051320.178727442876100
2.7835-2.88290.23351160.177327942910100
2.8829-2.99830.2361330.180127392872100
2.9983-3.13480.18381740.173226872861100
3.1348-3.30.20251580.17327402898100
3.3-3.50670.19251570.167127262883100
3.5067-3.77730.25841400.159227432883100
3.7773-4.15720.16141590.14727072866100
4.1572-4.75820.17171310.13227732904100
4.7582-5.99250.19591570.145527312888100
5.9925-44.91190.14811450.177527142859100
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)
10.72050.0406-0.00411.12670.5251.14990.02180.01870.0575-0.2189-0.08420.1362-0.0289-0.10670.04040.15230.0692-0.03830.0736-0.01920.2187-10.541536.4798-13.4177
23.8464-0.8239-1.33730.4520.84892.02050.1714-0.06710.3926-0.12210.0343-0.1669-0.17230.3837-0.17460.17080.04470.00020.1231-0.00630.29577.075335.9785-10.0248
30.60820.7616-0.06141.15210.26481.85450.0231-0.1270.13910.0013-0.05140.1166-0.2794-0.0453-0.02560.07270.0491-0.00980.1471-0.06210.2543-0.230351.712220.7581
41.713-0.83290.59061.8431-0.10941.44630.0314-0.1843-0.0967-0.0876-0.01410.1480.2026-0.19210.00470.0147-0.0016-0.00810.135-0.02930.2041-4.969533.101615.5499
51.148-1.56681.32972.8624-0.93912.39990.1093-0.3357-0.33830.1240.15330.52420.3101-0.364-0.19210.13420.0330.02870.19230.04830.33661.437624.113919.0695
60.34090.5972-0.34541.1887-0.07032.03450.0689-0.02160.0899-0.2655-0.0671-0.1642-0.22660.1643-0.03310.06140.0319-0.00980.0904-0.03630.2592.186746.88178.0909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 115 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 257 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 65 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 66 through 132 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 133 through 216 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 256 )B0

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