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- PDB-3u92: Crystal structure of the GluK3 ligand binding domain complex with... -

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Basic information

Entry
Database: PDB / ID: 3u92
TitleCrystal structure of the GluK3 ligand binding domain complex with kainate and zinc: P2221 form
ComponentsGlutamate receptor, ionotropic kainate 3
KeywordsMEMBRANE PROTEIN / ION CHANNEL
Function / homology
Function and homology information


Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / 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 ...Presynaptic function of Kainate receptors / regulation of presynaptic membrane potential / 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 / regulation of membrane potential / monoatomic ion transmembrane transport / 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 / axon / dendrite / glutamatergic synapse / 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
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor ionotropic, kainate 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKumar, J. / Mayer, M.L.
CitationJournal: Neuron / Year: 2012
Title: Zinc Potentiates GluK3 Glutamate Receptor Function by Stabilizing the Ligand Binding Domain Dimer Interface.
Authors: Veran, J. / Kumar, J. / Pinheiro, P.S. / Athane, A. / Mayer, M.L. / Perrais, D. / Mulle, C.
History
DepositionOct 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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_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.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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,12714
Polymers58,1072
Non-polymers1,02112
Water6,485360
1
A: Glutamate receptor, ionotropic kainate 3
B: Glutamate receptor, ionotropic kainate 3
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)118,25528
Polymers116,2134
Non-polymers2,04124
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area5640 Å2
ΔGint-448 kcal/mol
Surface area47000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.537, 55.654, 90.052
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
11A-325-

HOH

DetailsTHE OBSERVED BIOLOGICAL UNIT DOES NOT OCCUR FOR THE FULL LENGTH PROTEIN THEREFORE, IS NOT BIOLOGICALLY RELEVANT

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Components

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


Mass: 29053.371 Da / Num. of mol.: 2 / Fragment: unp residues 433-546 and 669-807
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK3 / Plasmid: PET22 modified / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B(DE3) / References: UniProt: P42264
#2: Chemical ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE / Kainic acid


Mass: 213.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15NO4 / Comment: neurotransmitter, agonist*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS ...THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK3. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (433-546 AND 669-807)

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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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 5% PEG 8K, 0.1 M Tris, 4 mM Kainate, 2 mM ZnAcetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45 Å / Num. all: 52357 / Num. obs: 52357 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 34
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.589 / Mean I/σ(I) obs: 2.9 / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S50

1s50


Resolution: 1.9→42.53 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2643 5.11 %RANDOM
Rwork0.1869 ---
all0.1887 51682 --
obs0.1887 51682 98.6 %-
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.585 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.5565 Å2-0 Å20 Å2
2---1.1264 Å2-0 Å2
3---11.683 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 0 40 360 4436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124170
X-RAY DIFFRACTIONf_angle_d1.0435612
X-RAY DIFFRACTIONf_dihedral_angle_d13.2211558
X-RAY DIFFRACTIONf_chiral_restr0.067620
X-RAY DIFFRACTIONf_plane_restr0.004702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8971-1.93160.30921340.26572379X-RAY DIFFRACTION93
1.9316-1.96870.30041500.24412523X-RAY DIFFRACTION98
1.9687-2.00890.27311530.23252484X-RAY DIFFRACTION98
2.0089-2.05260.2711370.22472563X-RAY DIFFRACTION98
2.0526-2.10030.26411440.2052529X-RAY DIFFRACTION99
2.1003-2.15290.28481390.19762530X-RAY DIFFRACTION98
2.1529-2.21110.20361350.19322562X-RAY DIFFRACTION99
2.2111-2.27610.2621390.18092550X-RAY DIFFRACTION99
2.2761-2.34960.23321310.1912580X-RAY DIFFRACTION99
2.3496-2.43350.24091500.19032561X-RAY DIFFRACTION99
2.4335-2.5310.20171190.19182584X-RAY DIFFRACTION99
2.531-2.64610.27331470.18812599X-RAY DIFFRACTION99
2.6461-2.78560.25521180.19412605X-RAY DIFFRACTION99
2.7856-2.96010.23411320.19492596X-RAY DIFFRACTION100
2.9601-3.18860.25361350.19522609X-RAY DIFFRACTION100
3.1886-3.50930.22541430.19592647X-RAY DIFFRACTION100
3.5093-4.01680.22411580.18582622X-RAY DIFFRACTION100
4.0168-5.05950.15131410.14052703X-RAY DIFFRACTION100
5.0595-42.54070.19421380.19022813X-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)
11.1617-0.30680.45980.2478-0.38171.2544-0.0016-0.12710.08580.0954-0.0361-0.2336-0.26630.06680.04970.2767-0.0539-0.07950.17940.01690.276444.777939.732615.2604
21.2976-0.74720.49182.4927-0.53690.2820.071-1.2391-0.24850.2272-0.03150.3838-0.1180.0406-0.02080.3003-0.0469-0.05660.5370.06330.26141.043825.593229.1067
30.8868-0.14810.30320.0888-0.19210.75620.11690.02180.07860.0123-0.1349-0.2336-0.03990.10150.06810.2404-0.0335-0.10180.19920.00350.281348.343531.290716.6951
40.2308-0.55320.09961.3205-0.27150.90470.24580.10950.3134-0.1139-0.2194-0.35940.01630.28630.01630.2352-0.0086-0.00050.2695-0.00710.304748.102834.0687-0.5403
50.1734-0.1279-0.37740.57390.32771.3371-0.0307-0.0111-0.10460.0406-0.00180.2668-0.0598-0.64710.01770.2489-0.0001-0.00090.41010.02880.27744.007219.857411.3963
61.57170.0508-0.26070.29030.00311.7332-0.1143-0.1126-0.37420.00990.0194-0.10180.2393-0.02680.04010.2637-0.0060.01170.2330.08550.345918.03669.308922.0412
71.40110.1696-0.03340.35-0.22770.4469-0.0832-0.4306-0.15260.02280.0192-0.0145-0.02640.20720.04080.23530.010.01490.36120.04470.272617.9915.347724.5367
80.4567-0.5011-0.54030.8240.69231.02420.1821-0.09840.001-0.1138-0.3570.2152-0.39240.0680.06010.3445-0.0422-0.01210.2623-0.05740.356520.01129.60317.9322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:136)
2X-RAY DIFFRACTION2(chain A and resid 137:165)
3X-RAY DIFFRACTION3(chain A and resid 166:230)
4X-RAY DIFFRACTION4(chain A and resid 231:256)
5X-RAY DIFFRACTION5(chain B and resid 3:32)
6X-RAY DIFFRACTION6(chain B and resid 33:161)
7X-RAY DIFFRACTION7(chain B and resid 162:237)
8X-RAY DIFFRACTION8(chain B and resid 238:256)

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