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- PDB-4nwd: Crystal structure of the kainate receptor GluK3 ligand-binding do... -

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Basic information

Entry
Database: PDB / ID: 4nwd
TitleCrystal structure of the kainate receptor GluK3 ligand-binding domain in complex with the agonist (2S,4R)-4-(3-Methylamino-3-oxopropyl)glutamic acid at 2.6 A resolution
ComponentsGlutamate receptor ionotropic, kainate 3
KeywordsMEMBRANE PROTEIN/AGONIST / kainate receptor / ligand binding domain / agonist / ionotropic glutamate receptor / MEMBRABE PROTEIN-AGONIST complex / MEMBRANE PROTEIN-AGONIST complex
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity ...Presynaptic function of Kainate receptors / cochlear hair cell ribbon synapse / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / G protein-coupled glutamate receptor signaling pathway / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / glutamate receptor signaling pathway / kainate selective glutamate receptor activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / perikaryon / chemical synaptic transmission / postsynaptic membrane / axon / dendrite / glutamatergic synapse / 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-2QD / : / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsVenskutonyte, R. / Larsen, A.P. / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4385
Polymers29,0921
Non-polymers3464
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.650, 68.650, 126.830
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 / 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
#2: Chemical ChemComp-2QD / (4R)-4-[3-(methylamino)-3-oxopropyl]-L-glutamic acid


Type: L-peptide linking / Mass: 232.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N2O5
#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.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 1.8 M NaH2PO4/K2HPO4, co-crystallized with (S)-glutamate, soaked with (2S,4R)-4-(3-Methylamino-3-oxopropyl)glutamic acid, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9974 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9974 Å / Relative weight: 1
ReflectionResolution: 2.6→38.546 Å / Num. all: 9923 / Num. obs: 9923 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 46.942 Å2 / Rsym value: 0.092 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.747.10.3821.81005014110.382100
2.74-2.917.10.2682.6943113230.268100
2.91-3.117.10.1694.2897312630.169100
3.11-3.367.10.1096.5838211820.109100
3.36-3.6870.0788.9763410850.078100
3.68-4.1170.0610.769679990.06100
4.11-4.756.90.06210.161478900.062100
4.75-5.816.80.0866.952257720.086100
5.81-8.226.50.0639.539956150.063100
8.22-38.5465.60.03318.121283830.03399

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S9E

3s9e


Resolution: 2.6→38.546 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8176 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2645 475 4.8 %random
Rwork0.2054 ---
obs0.2082 9889 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.33 Å2 / Biso mean: 50.3806 Å2 / Biso min: 14.22 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2019 0 19 49 2087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112083
X-RAY DIFFRACTIONf_angle_d1.4942804
X-RAY DIFFRACTIONf_chiral_restr0.077310
X-RAY DIFFRACTIONf_plane_restr0.008355
X-RAY DIFFRACTIONf_dihedral_angle_d13.606787
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs
2.6001-2.97620.30221500.2484305432043054
2.9762-3.74920.2791640.2218308632503086
3.7492-38.55020.24141610.1804327434353274
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)
12.8091-1.53180.0362.1828-0.59013.58050.15680.211-0.1171-0.38430.0567-0.03160.1304-0.01200.3628-0.0047-0.03280.3243-0.02960.3349-12.77343.3508-22.4114
23.80150.57061.18163.04330.78973.35690.38040.2095-0.48380.09570.0976-0.8930.69370.67370.15940.29780.1638-0.23640.2453-0.07990.1952-2.257734.6258-13.2637
32.7871-2.1528-1.23382.2620.83053.3028-0.1166-0.23480.38520.7273-0.11151.00220.4217-0.43350.00070.4975-0.0254-0.01090.47710.02350.3637-17.839238.6062-8.0584
42.7161.84040.67313.42931.06872.51110.3640.3202-0.910.67840.2606-0.89631.11550.46210.07430.81320.2065-0.35150.389-0.15520.7499-3.536120.9098-15.265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:44)A5 - 44
2X-RAY DIFFRACTION2(chain A and resid 45:127)A45 - 127
3X-RAY DIFFRACTION3(chain A and resid 227:258)A227 - 258
4X-RAY DIFFRACTION4(chain A and resid 128:226)A128 - 226

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