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- PDB-5o4f: Structure of GluK3 ligand-binding domain (S1S2) in complex with t... -

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Basic information

Entry
Database: PDB / ID: 5o4f
TitleStructure of GluK3 ligand-binding domain (S1S2) in complex with the agonist LM-12b at 2.10 A resolution
ComponentsGlutamate receptor ionotropic, kainate 3
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / KAINATE RECEPTOR / LIGAND-BINDING DOMAIN / GLUK3 / GLUR7 / AGONIST
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / 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 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 / 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 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-8VE / ACETATE ION / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsMoellerud, S. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: ACS Chem Neurosci / Year: 2017
Title: Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors.
Authors: Mllerud, S. / Pinto, A. / Marconi, L. / Frydenvang, K. / Thorsen, T.S. / Laulumaa, S. / Venskutonyte, R. / Winther, S. / Moral, A.M.C. / Tamborini, L. / Conti, P. / Pickering, D.S. / Kastrup, J.S.
History
DepositionMay 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 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_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.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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,70121
Polymers58,1852
Non-polymers1,51619
Water2,990166
1
B: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,97712
Polymers29,0921
Non-polymers88411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7249
Polymers29,0921
Non-polymers6318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.392, 56.205, 87.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-307-

ZN

21B-482-

HOH

31A-476-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 4:20 OR RESSEQ 22:26 OR RESSEQ...
211(CHAIN B AND (RESSEQ 4:20 OR RESSEQ 22:26 OR RESSEQ...

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Components

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Protein , 1 types, 2 molecules BA

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


Mass: 29092.453 Da / Num. of mol.: 2
Fragment: ligand-binding domain, UNP Residues 669-806,ligand-binding domain, UNP Residues 432-546
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 117-118). THE SEQUENCE MATCHES ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (RESIDUES 117-118). 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 / Production host: Escherichia coli (E. coli) / Variant (production host): Origami 2 / References: UniProt: P42264

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Non-polymers , 6 types, 185 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-8VE / (3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic acid


Mass: 213.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N3O4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: 15% PEG4000, 0.3 M Lithium sulfate, 5 mM zinc acetate, 0.1 M Bis-Tris-Propane pH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→131.392 Å / Num. obs: 38619 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.1 Å2 / Rsym value: 0.061 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.562 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.53 Å44.49 Å
Translation5.53 Å44.49 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PHASER2.5.1phasing
PDB_EXTRACT3.22data extraction
PHENIXmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U92

3u92


Resolution: 2.1→44.49 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.82
RfactorNum. reflection% reflection
Rfree0.215 1936 5.02 %
Rwork0.192 --
obs0.193 38592 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 60.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3993 0 75 166 4234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034157
X-RAY DIFFRACTIONf_angle_d0.6735594
X-RAY DIFFRACTIONf_dihedral_angle_d13.122514
X-RAY DIFFRACTIONf_chiral_restr0.042619
X-RAY DIFFRACTIONf_plane_restr0.004698
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A2656X-RAY DIFFRACTIONPOSITIONAL
12B2656X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15250.26041510.24782566X-RAY DIFFRACTION100
2.1525-2.21070.26961280.24032581X-RAY DIFFRACTION100
2.2107-2.27580.24671410.23242539X-RAY DIFFRACTION100
2.2758-2.34920.24841230.22812624X-RAY DIFFRACTION100
2.3492-2.43320.27361270.23012613X-RAY DIFFRACTION100
2.4332-2.53060.28381510.22462541X-RAY DIFFRACTION100
2.5306-2.64570.2451290.21342608X-RAY DIFFRACTION100
2.6457-2.78520.25531370.22292590X-RAY DIFFRACTION100
2.7852-2.95970.23711510.21862608X-RAY DIFFRACTION100
2.9597-3.18810.22261290.21552608X-RAY DIFFRACTION100
3.1881-3.50890.22761440.18752643X-RAY DIFFRACTION100
3.5089-4.01630.19781360.17052646X-RAY DIFFRACTION100
4.0163-5.0590.1571350.14512683X-RAY DIFFRACTION100
5.059-44.50030.19471540.18742806X-RAY DIFFRACTION99
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)
10.0627-0.01360.05590.02980.00320.0344-0.18120.1794-0.10060.10850.01650.04660.0105-0.1558-0.00010.3429-0.02480.01670.3850.03850.3027.993977.465110.2433
20.26220.0462-0.07720.06510.00730.0876-0.2501-0.0009-0.50690.07320.09220.02540.2362-0.10470.00550.4148-0.02280.12210.33480.03340.484715.854864.268715.1459
30.0017-0.0068-0.00120.00670.00880.0086-0.1239-0.1456-0.03660.0838-0.0444-0.0195-0.01410.0657-0.00020.75570.0861-0.01090.84180.0640.443123.363471.591144.8122
40.1690.08220.11850.0951-0.02130.1649-0.0736-0.4423-0.32480.09790.01360.0831-0.1386-0.0367-0.11840.38250.09920.07320.43950.2260.356717.719468.159733.6947
50.0435-0.02610.0060.0045-0.00050.0275-0.22220.1928-0.2023-0.0065-0.1201-0.0740.06010.2346-0.00050.382-0.04770.08620.40060.0110.40723.765170.82646.1469
60.00130.0102-0.00520.01460.00410.0085-0.10750.0741-0.0102-0.04310.02540.122-0.1932-0.06220.00010.3967-0.01530.00450.29080.04860.378719.664385.666116.6046
70.1875-0.1397-0.03380.0663-0.04390.35130.082-0.15420.54540.1323-0.0014-0.2898-0.086-0.0428-0.00060.3356-0.0456-0.01990.2986-0.02180.525343.311102.10413.401
80.1756-0.1676-0.08660.1850.02570.14710.7551-0.6579-0.42320.20750.2195-0.1570.6555-0.43020.78850.5527-0.3094-0.69120.7170.29230.147946.462778.619925.5105
90.4364-0.1065-0.1650.02390.05670.10350.5019-0.13520.10380.02980.0089-0.42910.48140.11490.21340.4716-0.0685-0.2950.3738-0.01260.428254.541684.217720.3954
100.00940.03890.04080.10910.12550.11870.11710.16280.30320.0841-0.0858-0.15240.0041-0.002200.32850.02850.02270.37260.07040.376243.11594.08063.0625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 4 THROUGH 47 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 48 THROUGH 115 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 116 THROUGH 132 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 133 THROUGH 212 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 213 THROUGH 238 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 239 THROUGH 255 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 4 THROUGH 105 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 106 THROUGH 163 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 164 THROUGH 212 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 213 THROUGH 256 )

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