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- PDB-6f28: Crystal structure of the kainate receptor GluK3 ligand binding do... -

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Basic information

Entry
Database: PDB / ID: 6f28
TitleCrystal structure of the kainate receptor GluK3 ligand binding domain in complex with (S)-1-[2'-Amino-2'-carboxyethyl]-6-methyl-5,7-dihydropyrrolo[3,4-d]pyrimidin-2,4(1H,3H)-dione at resolution 2.4A
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 / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity ...Presynaptic function of Kainate receptors / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / G protein-coupled glutamate receptor signaling pathway / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / glutamate receptor activity / kainate selective glutamate receptor activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / chemical synaptic transmission / perikaryon / axon / glutamatergic synapse / dendrite / 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-CG8 / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / struct_ncs_dom_lim
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
B: Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,22313
Polymers58,1852
Non-polymers1,03811
Water82946
1
A: Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4835
Polymers29,0921
Non-polymers3914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor ionotropic, kainate 3,Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7408
Polymers29,0921
Non-polymers6477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.039, 56.214, 87.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-302-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 6 through 257)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: CYS / End label comp-ID: CYS / Auth seq-ID: 6 - 257 / Label seq-ID: 6 - 257

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain A and resid 6 through 257)AA
2chain BBB

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 29092.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 119 AND 120 OF THE STRUCTURE). THE SEQUENCE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 119 AND 120 OF THE STRUCTURE). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (432-546, 669-806). THE FIRST THREE RESIDUES GLY-PRO-GLY ARE CLONING REMNANTS.
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

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Non-polymers , 5 types, 57 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CG8 / (2~{S})-2-azanyl-3-[6-methyl-2,4-bis(oxidanylidene)-5,7-dihydropyrrolo[3,4-d]pyrimidin-1-yl]propanoic acid


Mass: 254.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 20% PEG3350, 0.1M BisTrisPropane pH 8.4, 0.2M sodium sulfate, 5 mM zinc acetate

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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: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→28.374 Å / Num. obs: 25952 / % possible obs: 99.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 49.94 Å2 / Rpim(I) all: 0.027 / Rrim(I) all: 0.059 / Rsym value: 0.052 / Net I/av σ(I): 10.2 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.4-2.534.50.395237490.2090.4470.395100
2.53-2.684.40.262.835310.1380.2950.26100
2.68-2.874.40.1684.632990.0880.190.168100
2.87-3.14.40.0987.631210.0510.1110.098100
3.1-3.394.40.06211.328670.0330.070.062100
3.39-3.794.40.04613.426080.0240.0520.046100
3.79-4.384.40.03816.523220.020.0430.038100
4.38-5.374.30.03517.119730.0180.0390.035100
5.37-7.594.20.03716.915740.020.0420.037100
7.59-28.3743.80.0318.39080.0170.0350.0397.7

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mh5

4mh5


Resolution: 2.4→28.374 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.07
RfactorNum. reflection% reflection
Rfree0.2216 1318 5.08 %
Rwork0.1954 --
obs0.1967 25932 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 161.66 Å2 / Biso mean: 70.1164 Å2 / Biso min: 32.24 Å2
Refinement stepCycle: final / Resolution: 2.4→28.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4022 0 49 46 4117
Biso mean--69.53 52.18 -
Num. residues----506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034143
X-RAY DIFFRACTIONf_angle_d0.5675585
X-RAY DIFFRACTIONf_chiral_restr0.042614
X-RAY DIFFRACTIONf_plane_restr0.004699
X-RAY DIFFRACTIONf_dihedral_angle_d16.9832494
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3024X-RAY DIFFRACTION9.518TORSIONAL
12B3024X-RAY DIFFRACTION9.518TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.49610.29331380.289727042842
2.4961-2.60960.2721480.259426732821
2.6096-2.74710.25571220.248427162838
2.7471-2.9190.28691470.258527062853
2.919-3.14410.27911530.243827032856
3.1441-3.460.23041550.218227092864
3.46-3.95950.22611480.190727372885
3.9595-4.98420.17251450.14627612906
4.9842-28.37550.20211620.169329053067
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)
12.0181-1.7308-0.91911.79180.17874.3375-0.17780.06632.1037-0.13430.34151.4253-0.7661-0.5834-0.15740.54920.2036-0.04010.535-0.02141.4148-52.4571-5.9388-10.5265
25.1011.3661.57411.88570.5032.88770.0530.86580.3552-0.47960.01250.251-0.00720.2322-0.06910.41350.1225-0.07280.46480.08040.4328-42.8389-21.8484-20.1047
33.51061.94024.73322.68541.26367.99830.35250.27930.443-0.3565-0.17780.69720.2359-0.5396-0.14230.40540.0523-0.17370.4670.00660.6088-55.061-29.0889-18.2632
44.70123.5235-0.72515.4711-1.59085.46310.2134-0.44620.6780.1333-0.18920.46870.0545-0.22540.01540.24640.04530.01250.2807-0.0720.3746-42.979-18.348-3.0471
53.73951.601-0.20453.40920.66346.0813-0.14570.0626-0.6172-0.1745-0.0587-0.69640.07490.78460.06960.35850.10970.06550.5003-0.0310.5609-8.119-38.2843-10.4871
64.9377-3.3961.61873.44571.03785.7647-0.5129-0.2389-1.5291-0.29020.2443-0.30841.40520.13220.05690.79180.01550.32970.4359-0.01891.1509-16.5727-52.6225-12.6022
75.58280.7932.93185.4421.15419.2561-0.22970.78350.2439-0.88980.29610.2095-0.6157-0.3623-0.13640.416-0.08230.01350.3396-0.04580.4928-23.1044-37.6808-30.8462
84.89311.21150.41066.55942.51446.5669-0.0940.9217-1.0112-0.40450.3169-0.79340.32360.2627-0.25330.5915-0.08080.06980.6293-0.2560.6437-18.6814-44.183-34.7331
96.33510.0993-1.5645.8617-2.82637.7438-0.1672-0.2083-0.13160.1210.08790.0183-0.1548-0.19870.03230.27620.00380.04410.3343-0.08550.3687-21.7281-34.9618-10.8778
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 36 )A5 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 173 )A37 - 173
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 214 )A174 - 214
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 258 )A215 - 258
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 67 )B6 - 67
6X-RAY DIFFRACTION6chain 'B' and (resid 68 through 103 )B68 - 103
7X-RAY DIFFRACTION7chain 'B' and (resid 104 through 124 )B104 - 124
8X-RAY DIFFRACTION8chain 'B' and (resid 125 through 214 )B125 - 214
9X-RAY DIFFRACTION9chain 'B' and (resid 215 through 257 )B215 - 257

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