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

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Basic information

Entry
Database: PDB / ID: 5mfq
TitleCrystal structure of the GluK1 ligand-binding domain in complex with kainate and BPAM-344 at 1.90 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 / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / nervous system development / presynaptic membrane / 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-2J9 / 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: 1.9 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 2.0Jun 27, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_src_gen / pdbx_nonpoly_scheme / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity.details / _entity.pdbx_fragment / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_isoform / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 2.1Jan 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 2.2Nov 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

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)59,63212
Polymers58,2172
Non-polymers1,41510
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-26 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.013, 71.013, 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,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.,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 BL21(DE3) (bacteria) / Variant (production host): ORIGAMI 2 / References: UniProt: P22756

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Non-polymers , 6 types, 592 molecules

#2: Chemical ChemComp-2J9 / 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide


Mass: 242.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11FN2O2S
#3: Chemical ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE


Mass: 213.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15NO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15.2 % 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: 0.97916 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.9→29.429 Å / Num. obs: 48600 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 18.22 Å2 / Rsym value: 0.072 / Net I/av σ(I): 8.04 / Net I/σ(I): 18.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-28.20.3162.21100
2-2.128.20.2013.51100
2.12-2.278.20.14151100
2.27-2.458.20.116.41100
2.45-2.698.10.097.71100
2.69-38.10.0699.51100
3-3.478.10.05710.91100
3.47-4.2580.04712.81100
4.25-6.017.80.0414.61100
6.01-29.42970.03615.7198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.45 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.43 Å
Translation2.5 Å29.43 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data 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: 1.9→29.429 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.72
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 2452 5.06 %Random selection
Rwork0.1551 ---
obs0.1571 48489 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.94 Å2 / Biso mean: 23.11 Å2 / Biso min: 5.17 Å2
Refinement stepCycle: final / Resolution: 1.9→29.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 91 582 4715
Biso mean--25.44 32.09 -
Num. residues----507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064297
X-RAY DIFFRACTIONf_angle_d1.0535820
X-RAY DIFFRACTIONf_chiral_restr0.075640
X-RAY DIFFRACTIONf_plane_restr0.005730
X-RAY DIFFRACTIONf_dihedral_angle_d13.7991666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93660.24181530.180925182671100
1.9366-1.97610.25631300.174924842614100
1.9761-2.0190.21111440.156524962640100
2.019-2.0660.21341350.152425052640100
2.066-2.11760.2051330.152425212654100
2.1176-2.17490.18191360.155225102646100
2.1749-2.23890.21131360.156725222658100
2.2389-2.31110.21461300.154725162646100
2.3111-2.39370.20641360.156425402676100
2.3937-2.48940.23221220.164725312653100
2.4894-2.60270.23741240.164225682692100
2.6027-2.73980.20511320.164825622694100
2.7398-2.91130.23881560.168225182674100
2.9113-3.13590.2041410.16925732714100
3.1359-3.4510.19171230.154926042727100
3.451-3.94940.16671540.141326002754100
3.9494-4.97190.14061380.125226472785100
4.9719-29.43210.16941290.16392822295199
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)
10.04760.01080.01660.1925-0.08420.08840.0490.0337-0.0043-0.2926-0.033-0.02260.1640.00840.0940.21760.03610.02690.0708-0.03070.0882-6.020123.5493-15.6649
20.12270.0962-0.11710.0926-0.04040.3632-0.01980.0050.01390.0004-00.00870.00630.047-0.0160.0752-0.01170.01930.0596-0.0010.08371.919340.2373-10.6528
30.0673-0.0305-0.09290.05850.07270.15130.0028-0.0978-0.01930.0105-0.0024-0.0258-0.0509-0.0726-00.0874-0.0060.01190.0903-0.00650.0872-13.192538.558420.0453
40.155-0.03830.01890.04180.11360.40120.03410.0030.0232-0.0392-0.02270.00450.09410.13170.02280.0579-0.00220.02640.07550.0090.06274.996934.036415.2633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 432 through 520 )A432 - 520
2X-RAY DIFFRACTION2chain 'A' and (resid 521 through 804 )A521 - 804
3X-RAY DIFFRACTION3chain 'B' and (resid 432 through 520 )B432 - 520
4X-RAY DIFFRACTION4chain 'B' and (resid 521 through 805 )B521 - 805

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