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- PDB-4nwc: Crystal structure of the GluK3 ligand-binding domain (S1S2) in co... -

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Basic information

Entry
Database: PDB / ID: 4nwc
TitleCrystal structure of the GluK3 ligand-binding domain (S1S2) in complex with the agonist (2S,4R)-4-(3-Methoxy-3-oxopropyl)glutamic acid at 2.01 A resolution.
ComponentsGlutamate receptor ionotropic, kainate 3
KeywordsMEMBRANE PROTEIN / RECEPTOR/Agonist / Kainate receptor ligand-binding domain / Agonist / Ionotropic glutamate receptor / RECEPTOR-Agonist complex
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
(2S,4R)-4-(3-Methoxy-3-oxopropyl) glutamic acid / : / PHOSPHATE ION / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.012 Å
AuthorsLarsen, A.P. / Venskutonyte, R. / Frydenvang, K. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: Chemmedchem / Year: 2014
Title: Molecular Recognition of Two 2,4-syn-Functionalized (S)-Glutamate Analogues by the Kainate Receptor GluK3 Ligand Binding Domain.
Authors: Venskutonyte, R. / Larsen, A.P. / Frydenvang, K. / Gajhede, M. / Sagot, E. / Assaf, Z. / Gefflaut, T. / Pickering, D.S. / Bunch, L. / Kastrup, J.S.
#1: Journal: J.Struct.Biol. / Year: 2011
Title: Binding site and interlobe interactions of the ionotropic glutamate receptor GluK3 ligand binding domain revealed by high resolution crystal structure in complex with (S)-glutamate.
Authors: Venskutonyte, R. / Frydenvang, K. / Gajhede, M. / Bunch, L. / Pickering, D.S. / Kastrup, J.S.
History
DepositionDec 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Aug 9, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen / software / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 20, 2023Group: 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_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,5346
Polymers29,0921
Non-polymers4425
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glutamate receptor ionotropic, kainate 3
hetero molecules

A: Glutamate receptor ionotropic, kainate 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,06912
Polymers58,1852
Non-polymers88410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4480 Å2
ΔGint-49 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.810, 67.810, 126.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-901-

K

21A-1173-

HOH

31A-1220-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 29092.453 Da / Num. of mol.: 1 / Fragment: unp residues 432-546 and unp residues 669-806
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur7, Grik3 / Plasmid: pOPINJ / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P42264

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Non-polymers , 5 types, 235 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-2QE / (2S,4R)-4-(3-Methoxy-3-oxopropyl) glutamic acid / (4R)-4-(3-methoxy-3-oxopropyl)-L-glutamic acid


Mass: 233.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15NO6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.8M sodium/potassium phosphate, co-crystallized with (S)-glutamate, soaked with 10mM (2S,4R)-4-(3-Methoxy-3-oxopropyl)glutamic acid, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.012→38.24 Å / Num. all: 20406 / Num. obs: 20406 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 17.19 Å2 / Rsym value: 0.098 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.01-2.126.80.2842.50.2841100
2.12-2.256.80.2073.30.2071100
2.25-2.46.80.164.40.161100
2.4-2.66.80.1265.70.1261100
2.6-2.856.70.1076.50.1071100
2.85-3.186.80.0847.70.0841100
3.18-3.676.70.0738.60.0731100
3.67-4.56.60.0748.30.0741100
4.5-6.366.40.0688.50.0681100
6.36-38.245.70.05210.80.052199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.14 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.24 Å
Translation2.5 Å38.24 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3S9E

3s9e


Resolution: 2.012→19.931 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.2 / σ(F): 1.39 / Phase error: 18.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 1042 5.12 %
Rwork0.1664 --
obs0.1688 20333 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.7724 Å2
Refinement stepCycle: LAST / Resolution: 2.012→19.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 24 230 2280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132127
X-RAY DIFFRACTIONf_angle_d1.0582849
X-RAY DIFFRACTIONf_dihedral_angle_d14.103806
X-RAY DIFFRACTIONf_chiral_restr0.071316
X-RAY DIFFRACTIONf_plane_restr0.004358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.012-2.1180.23911560.17692691X-RAY DIFFRACTION100
2.118-2.25050.22041640.16452653X-RAY DIFFRACTION100
2.2505-2.4240.21931380.16652733X-RAY DIFFRACTION100
2.424-2.66740.23681330.17332736X-RAY DIFFRACTION100
2.6674-3.05220.20381460.17652739X-RAY DIFFRACTION100
3.0522-3.8410.20121530.1592788X-RAY DIFFRACTION100
3.841-19.93210.2091520.16162951X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 6.7421 Å / Origin y: 31.0044 Å / Origin z: 14.7921 Å
111213212223313233
T0.1412 Å2-0.0208 Å2-0.039 Å2-0.1394 Å20.0162 Å2--0.1217 Å2
L1.0663 °20.3438 °20.1482 °2-1.9848 °20.0245 °2--0.81 °2
S0.067 Å °-0.0716 Å °-0.1554 Å °-0.0459 Å °-0.0171 Å °0.1222 Å °0.1932 Å °-0.1014 Å °-0.0342 Å °
Refinement TLS groupSelection details: all

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