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- PDB-6f29: Crystal structure of the kainate receptor GluK3 ligand binding do... -

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Basic information

Entry
Database: PDB / ID: 6f29
TitleCrystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-1-[2-Amino-2-carboxyethyl]-5,7-dihydrothieno[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 2.6A
ComponentsGlutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor / GluK3 / ligand binding domain / membrane protein.
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway ...Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / G protein-coupled glutamate receptor signaling pathway / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor activity / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / monoatomic ion transmembrane transport / chemical synaptic transmission / perikaryon / postsynaptic membrane / axon / glutamatergic synapse / dendrite / 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-CGW / : / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVenskutonyte, R. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: J. Med. Chem. / Year: 2018
Title: ( S)-2-Amino-3-(5-methyl-3-hydroxyisoxazol-4-yl)propanoic Acid (AMPA) and Kainate Receptor Ligands: Further Exploration of Bioisosteric Replacements and Structural and Biological Investigation.
Authors: Brogi, S. / Brindisi, M. / Butini, S. / Kshirsagar, G.U. / Maramai, S. / Chemi, G. / Gemma, S. / Campiani, G. / Novellino, E. / Fiorenzani, P. / Pinassi, J. / Aloisi, A.M. / Gynther, M. / ...Authors: Brogi, S. / Brindisi, M. / Butini, S. / Kshirsagar, G.U. / Maramai, S. / Chemi, G. / Gemma, S. / Campiani, G. / Novellino, E. / Fiorenzani, P. / Pinassi, J. / Aloisi, A.M. / Gynther, M. / Venskutonyte, R. / Han, L. / Frydenvang, K. / Kastrup, J.S. / Pickering, D.S.
History
DepositionNov 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5347
Polymers29,0921
Non-polymers4426
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-27 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.040, 68.040, 126.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-303-

K

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Components

#1: Protein Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3 / GluK3 / Glutamate receptor 7 / GluR7


Mass: 29092.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 119 AND 120 OF THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 119 AND 120 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (432-546, 669-806)
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik3, Glur7 / Plasmid: POPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P42264
#2: Chemical ChemComp-CGW / (2~{S})-2-azanyl-3-[2,4-bis(oxidanylidene)-5,7-dihydrothieno[3,4-d]pyrimidin-1-yl]propanoic acid


Mass: 257.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N3O4S
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#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.: 47 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 1.8M sodium/potassium phosphate pH 8.2

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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 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→35.915 Å / Num. obs: 9697 / % possible obs: 99.8 % / Redundancy: 7.7 % / Biso Wilson estimate: 33.71 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.116 / Rsym value: 0.108 / Net I/av σ(I): 5.8 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.6-2.747.80.4331.813830.160.4630.433100
2.74-2.917.80.312.513100.1150.3320.31100
2.91-3.117.80.2033.712400.0750.2170.203100
3.11-3.367.80.1325.411450.050.1420.132100
3.36-3.687.80.0986.810690.0370.1050.098100
3.68-4.117.70.0837.29790.0320.0890.08399.8
4.11-4.757.70.0797.58570.030.0840.07999.7
4.75-5.817.50.078.27580.0260.0750.0799.5
5.81-8.227.20.05410.25930.0210.0580.05499.3
8.22-35.9156.40.04411.63630.0170.0470.04497.9

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MH5

4mh5


Resolution: 2.6→35.915 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 21.26
RfactorNum. reflection% reflection
Rfree0.2481 467 4.82 %
Rwork0.1921 --
obs0.1947 9695 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.61 Å2 / Biso mean: 47.0813 Å2 / Biso min: 9.82 Å2
Refinement stepCycle: final / Resolution: 2.6→35.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 22 47 2088
Biso mean--43.19 33.37 -
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072077
X-RAY DIFFRACTIONf_angle_d0.9222800
X-RAY DIFFRACTIONf_chiral_restr0.052308
X-RAY DIFFRACTIONf_plane_restr0.005352
X-RAY DIFFRACTIONf_dihedral_angle_d7.9391251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.97610.26861660.225729793145100
2.9761-3.7490.27991540.203630433197100
3.749-35.91890.21791470.17263206335399
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)
13.213-1.03690.8213.0824-0.19773.0780.17870.4393-0.1008-0.1874-0.0071-0.31960.2370.5712-0.11290.19210.0122-0.00230.183-0.05970.1553-5.935942.3454-19.3743
23.49242.13291.37591.91090.26482.76090.44390.1605-0.90720.52350.0914-0.57820.92210.26-0.2470.4820.123-0.26790.1824-0.04860.4004-6.19725.3947-12.297
35.27262.303-0.06159.14856.05584.51850.1731.0271-0.4764-0.1447-0.38952.03720.5434-0.81890.07360.87250.0368-0.02140.4256-0.20750.3809-24.636424.3854-17.8742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 5 through 87 )A5 - 87
2X-RAY DIFFRACTION2chain A and (resid 88 through 251 )A88 - 251
3X-RAY DIFFRACTION3chain A and (resid 252 through 258 )A252 - 258

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