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- PDB-3qlt: Crystal structure of a GluK2 (GluR6) glycan wedge homodimer assembly -

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Basic information

Entry
Database: PDB / ID: 3qlt
TitleCrystal structure of a GluK2 (GluR6) glycan wedge homodimer assembly
ComponentsGlutamate receptor, ionotropic kainate 2
KeywordsMEMBRANE PROTEIN / Glycosylation
Function / homology
Function and homology information


mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor complex / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / regulation of JNK cascade ...mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor complex / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / regulation of JNK cascade / inhibitory postsynaptic potential / receptor clustering / kainate selective glutamate receptor activity / extracellularly glutamate-gated ion channel activity / modulation of excitatory postsynaptic potential / ionotropic glutamate receptor complex / positive regulation of synaptic transmission / behavioral fear response / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / hippocampal mossy fiber to CA3 synapse / SNARE binding / PDZ domain binding / synaptic transmission, glutamatergic / excitatory postsynaptic potential / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular calcium ion homeostasis / terminal bouton / positive regulation of neuron apoptotic process / presynaptic membrane / neuron apoptotic process / scaffold protein binding / chemical synaptic transmission / negative regulation of neuron apoptotic process / perikaryon / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / ubiquitin protein ligase binding / synapse / dendrite / glutamatergic synapse / identical protein binding / membrane / plasma membrane
Similarity search - Function
Response regulator / 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 ...Response regulator / 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 I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.988 Å
AuthorsKumar, J. / Mayer, M.L.
CitationJournal: Neuron / Year: 2011
Title: Structure and assembly mechanism for heteromeric kainate receptors.
Authors: Kumar, J. / Schuck, P. / Mayer, M.L.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor, ionotropic kainate 2
B: Glutamate receptor, ionotropic kainate 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9748
Polymers89,6462
Non-polymers1,3276
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-2 kcal/mol
Surface area32130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.805, 191.805, 47.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLUchain B and (resseq 4:12 or resseq 19:41 or resseq...BB4 - 124 - 12
12METMETPROPROchain B and (resseq 4:12 or resseq 19:41 or resseq...BB19 - 4119 - 41
13THRTHRPROPROchain B and (resseq 4:12 or resseq 19:41 or resseq...BB43 - 17443 - 174
14ASPASPGLUGLUchain B and (resseq 4:12 or resseq 19:41 or resseq...BB176 - 268176 - 268
15PROPROGLUGLUchain B and (resseq 4:12 or resseq 19:41 or resseq...BB276 - 384276 - 384
21VALVALGLUGLUchain A and (resseq 4:12 or resseq 19:41 or resseq...AA4 - 124 - 12
22METMETPROPROchain A and (resseq 4:12 or resseq 19:41 or resseq...AA19 - 4119 - 41
23THRTHRPROPROchain A and (resseq 4:12 or resseq 19:41 or resseq...AA43 - 17443 - 174
24ASPASPGLUGLUchain A and (resseq 4:12 or resseq 19:41 or resseq...AA176 - 268176 - 268
25PROPROGLUGLUchain A and (resseq 4:12 or resseq 19:41 or resseq...AA276 - 384276 - 384

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Components

#1: Protein Glutamate receptor, ionotropic kainate 2 / Glutamate receptor 6 / GluR-6 / GluR6


Mass: 44823.172 Da / Num. of mol.: 2 / Mutation: A213N,G215S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur6, Grik2 / Plasmid: PRK-IRES_EGFP / Cell line (production host): HEK 293 GNTI(-) / Production host: Homo Sapiens (human) / References: UniProt: P42260
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8K, 20% ethylene glycol, 0.02 M each 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4 butanediol, 1,3-propanediol, and 0.1 M MOPS/HEPES-Na, pH 7.5, VAPOR DIFFUSION, ...Details: 10% PEG 8K, 20% ethylene glycol, 0.02 M each 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4 butanediol, 1,3-propanediol, and 0.1 M MOPS/HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 24, 2009
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.988→50 Å / Num. all: 17783 / Num. obs: 17783 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 87.84 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 16
Reflection shellResolution: 2.99→3.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 2 / Num. unique all: 1764 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H6G

3h6g


Resolution: 2.988→47.951 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2932 846 5.04 %random
Rwork0.2416 ---
all0.2441 16775 --
obs0.2441 16775 94.36 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.198 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.0935 Å2-0 Å20 Å2
2---11.0935 Å2-0 Å2
3---22.187 Å2
Refinement stepCycle: LAST / Resolution: 2.988→47.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5886 0 84 0 5970
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036103
X-RAY DIFFRACTIONf_angle_d0.6088250
X-RAY DIFFRACTIONf_dihedral_angle_d12.4922243
X-RAY DIFFRACTIONf_chiral_restr0.038937
X-RAY DIFFRACTIONf_plane_restr0.0021033
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2918X-RAY DIFFRACTIONPOSITIONAL0.013
12A2918X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9884-3.17560.4761280.3492324X-RAY DIFFRACTION84
3.1756-3.42080.40661460.30952492X-RAY DIFFRACTION90
3.4208-3.76490.32611370.27272665X-RAY DIFFRACTION96
3.7649-4.30940.27471570.21742729X-RAY DIFFRACTION98
4.3094-5.42820.26481500.20552798X-RAY DIFFRACTION99
5.4282-47.95740.23281280.22752921X-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)
11.8053-0.94530.70472.832-0.74620.34780.5755-0.6-0.47940.0977-0.14370.87170.0780.0607-0.36390.2929-0.0231-0.08980.4231-0.19790.8584-25.4562-49.739-17.9025
20.9321-0.66860.7661.1802-0.10870.99910.2525-0.00650.3776-0.0015-0.46330.24340.0037-0.07580.0430.2761-0.01750.18930.2699-0.18210.3654-4.042-26.4295-12.1591
31.045-0.39880.44531.9322-0.0090.19850.46480.209-0.1507-0.0188-0.54120.83450.0551-0.09360.10670.22660.1012-0.07840.3213-0.31370.4171-23.4455-37.8734-25.0149
40.9356-0.4218-0.10840.59540.23020.14690.3857-0.1219-0.8215-0.2301-0.38670.13840.143-0.1828-0.04280.3474-0.1529-0.15830.29310.18540.7733-4.8865-67.876-5.8162
52.7819-0.2526-0.33081.1158-0.23040.84160.3459-0.1897-0.3304-0.263-0.3315-0.0806-0.21390.05210.14510.37440.08050.20920.21910.04890.205816.1718-47.9768-19.0241
63.54890.8764-1.17540.6651-0.62831.55920.0542-0.3812-1.05740.262-0.5062-0.39140.33940.3020.3770.2734-0.1644-0.05660.17210.19720.30947.3211-64.7477-0.9328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:122)A4 - 122
2X-RAY DIFFRACTION2(chain A and resid 123:249) or (chain D and resid 2:3)A123 - 249
3X-RAY DIFFRACTION2(chain A and resid 123:249) or (chain D and resid 2:3)D2 - 3
4X-RAY DIFFRACTION3(chain A and resid 250:384) or (chain D and resid 4:5)A250 - 384
5X-RAY DIFFRACTION3(chain A and resid 250:384) or (chain D and resid 4:5)D4 - 5
6X-RAY DIFFRACTION4(chain B and resid 4:124)B4 - 124
7X-RAY DIFFRACTION5(chain B and resid 125:249) or (chain C and resid 2)B125 - 249
8X-RAY DIFFRACTION5(chain B and resid 125:249) or (chain C and resid 2)A2 - 397
9X-RAY DIFFRACTION6(chain B and resid 250:384) or (chain C and resid 4)B250 - 384
10X-RAY DIFFRACTION6(chain B and resid 250:384) or (chain C and resid 4)B4 - 397

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