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- PDB-3qlv: Crystal structure of the GluK2/GluK5 (GluR6/KA2) ATD tetramer assembly -

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Basic information

Entry
Database: PDB / ID: 3qlv
TitleCrystal structure of the GluK2/GluK5 (GluR6/KA2) ATD tetramer assembly
Components
  • Glutamate receptor, ionotropic kainate 2
  • Glutamate receptor, ionotropic kainate 5
KeywordsMEMBRANE PROTEIN / Glycosylation
Function / homology
Function and homology information


regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / ubiquitin conjugating enzyme binding ...regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / 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 / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / 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 / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / SNARE binding / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / cellular response to glucose stimulus / establishment of localization in cell / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / SH3 domain binding / intracellular calcium ion homeostasis / terminal bouton / positive regulation of neuron apoptotic process / presynaptic membrane / neuron apoptotic process / scaffold protein binding / perikaryon / chemical synaptic transmission / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / ubiquitin protein ligase binding / synapse / dendrite / glutamatergic synapse / endoplasmic reticulum / 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 / Glutamate receptor ionotropic, kainate 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.94 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 1.2Mar 31, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details
Revision 1.3Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 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 5
B: Glutamate receptor, ionotropic kainate 5
C: Glutamate receptor, ionotropic kainate 2
D: Glutamate receptor, ionotropic kainate 2
E: Glutamate receptor, ionotropic kainate 5
F: Glutamate receptor, ionotropic kainate 2
G: Glutamate receptor, ionotropic kainate 5
H: Glutamate receptor, ionotropic kainate 2
I: Glutamate receptor, ionotropic kainate 5
J: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)442,74110
Polymers442,74110
Non-polymers00
Water00
1
A: Glutamate receptor, ionotropic kainate 5
B: Glutamate receptor, ionotropic kainate 5
C: Glutamate receptor, ionotropic kainate 2
D: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)177,0974
Polymers177,0974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Glutamate receptor, ionotropic kainate 5
F: Glutamate receptor, ionotropic kainate 2
G: Glutamate receptor, ionotropic kainate 5
H: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)177,0974
Polymers177,0974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Glutamate receptor, ionotropic kainate 5
J: Glutamate receptor, ionotropic kainate 2

I: Glutamate receptor, ionotropic kainate 5
J: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)177,0974
Polymers177,0974
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
4
A: Glutamate receptor, ionotropic kainate 5
C: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area33480 Å2
MethodPISA
5
B: Glutamate receptor, ionotropic kainate 5
D: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-15 kcal/mol
Surface area33560 Å2
MethodPISA
6
E: Glutamate receptor, ionotropic kainate 5
F: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-16 kcal/mol
Surface area33330 Å2
MethodPISA
7
G: Glutamate receptor, ionotropic kainate 5
H: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area33490 Å2
MethodPISA
8
I: Glutamate receptor, ionotropic kainate 5
J: Glutamate receptor, ionotropic kainate 2


Theoretical massNumber of molelcules
Total (without water)88,5482
Polymers88,5482
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-14 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)366.552, 109.176, 155.469
Angle α, β, γ (deg.)90.00, 97.54, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
12
22
32
42
52

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain C and (resseq 10:35 or resseq 45: 104 or...
211chain D and (resseq 10:35 or resseq 45: 104 or...
311chain F and (resseq 10:35 or resseq 45: 104 or...
411chain H and (resseq 10:35 or resseq 45: 104 or...
511chain J and (resseq 10:35 or resseq 45: 104 or...
112chain A and (resseq 3:10 or resseq 22:37 or resseq...
212chain B and (resseq 3:10 or resseq 22:37 or resseq...
312chain E and (resseq 3:10 or resseq 22:37 or resseq...
412chain G and (resseq 3:10 or resseq 22:37 or resseq...
512chain I and (resseq 3:10 or resseq 22:37 or resseq...

NCS ensembles :
ID
1
2

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Components

#1: Protein
Glutamate receptor, ionotropic kainate 5 / Glutamate receptor KA-2 / KA2


Mass: 43798.176 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik5 / Plasmid: PRK-IRES_EGFP / Cell line (production host): HEK 293 GNTI(-) / Production host: Homo Sapiens (human) / References: UniProt: Q63273
#2: Protein
Glutamate receptor, ionotropic kainate 2 / Glutamate receptor 6 / GluR-6 / GluR6


Mass: 44750.121 Da / Num. of mol.: 5
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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.68 %
Crystal growTemperature: 293 K / pH: 8
Details: 10% Ethylene Glycol, 0.1 M HEPES, 5% PEG 8K, pH 8.0, 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
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: 3.94→50 Å / Num. obs: 54061 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 13.3 % / Biso Wilson estimate: 131 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 18.6
Reflection shellResolution: 3.95→4.1 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OM0 AND 3H6H

3om0

3h6h


Resolution: 3.94→48.95 Å / SU ML: 0.5 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 2595 5.1 %
Rwork0.264 --
obs0.264 50913 94.1 %
all-50913 -
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 107.93 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.0599 Å20 Å214.6265 Å2
2--23.7176 Å20 Å2
3----5.6576 Å2
Refinement stepCycle: LAST / Resolution: 3.94→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29634 0 0 0 29634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00530270
X-RAY DIFFRACTIONf_angle_d0.59340955
X-RAY DIFFRACTIONf_dihedral_angle_d13.14911215
X-RAY DIFFRACTIONf_chiral_restr0.0424655
X-RAY DIFFRACTIONf_plane_restr0.0035235
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C2395X-RAY DIFFRACTIONPOSITIONAL
12D2395X-RAY DIFFRACTIONPOSITIONAL0.014
13F2395X-RAY DIFFRACTIONPOSITIONAL0.052
14H2395X-RAY DIFFRACTIONPOSITIONAL0.004
15J2395X-RAY DIFFRACTIONPOSITIONAL0.061
21A2277X-RAY DIFFRACTIONPOSITIONAL
22B2277X-RAY DIFFRACTIONPOSITIONAL0.013
23E2277X-RAY DIFFRACTIONPOSITIONAL0.053
24G2277X-RAY DIFFRACTIONPOSITIONAL0.021
25I2277X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.942-4.08280.34712120.36334206X-RAY DIFFRACTION82
4.0828-4.24620.32992620.32354461X-RAY DIFFRACTION88
4.2462-4.43930.34992460.2954631X-RAY DIFFRACTION90
4.4393-4.67320.28492450.26294773X-RAY DIFFRACTION94
4.6732-4.96570.27312720.24434866X-RAY DIFFRACTION95
4.9657-5.34870.27572670.25384929X-RAY DIFFRACTION96
5.3487-5.88610.34252690.28714969X-RAY DIFFRACTION97
5.8861-6.7360.29972780.2735076X-RAY DIFFRACTION98
6.736-8.47950.2382720.21185139X-RAY DIFFRACTION99
8.4795-48.95310.24062720.25395268X-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)
11.26390.5596-0.73511.3374-0.77831.0576-0.19370.3449-0.1670.0315-0.24050.40040.1642-0.1235-0.00160.54370.0326-0.24870.9223-0.33270.4841-9.8529-33.303349.767
20.3847-0.23180.64931.75350.92212.020.3416-0.0888-0.2348-0.0354-0.1135-0.1353-0.21520.49890.00010.5287-0.02860.02060.95370.11950.769181.4568-14.921183.9502
32.5393-0.6960.07912.08430.7250.48380.00010.13640.3859-0.0580.04440.0897-0.04760.129200.6911-0.0518-0.11530.78820.14880.57969.9516-6.75361.5578
41.4823-0.38760.13081.6259-1.3451.10860.0821-0.0823-0.13390.1104-0.19090.08630.0388-0.2895-00.7192-0.0833-0.01090.6040.05450.763253.1759-34.877391.0049
52.26581.2138-0.14442.43180.82990.3105-0.18590.5209-0.037-0.14790.24240.39810.2769-0.15190.00010.77970.1714-0.04941.08040.31710.820735.1769-50.9644-11.8811
62.45190.05290.4219-0.0643-0.01410.40810.1263-0.48930.21210.3932-0.08040.04630.0734-0.072-00.8230.2460.19140.7190.06070.552245.3341-45.300721.1019
70.9093-0.0095-0.11550.828-1.00021.10250.08430.15820.09350.5488-0.1283-0.58810.01410.3508-01.061-0.2525-0.13920.87470.04291.3243117.406-39.754642.2448
81.3221-0.81350.22981.9242-0.12520.18540.03760.42170.08310.0101-0.04960.07010.2770.1456-00.93570.04460.04320.9588-0.10520.8031102.3773-62.933620.4746
90.22880.31760.19520.35370.41352.18-0.1097-0.3488-1.04930.29290.32910.70290.63940.224201.21350.5091-0.05280.73680.1862.558148.492410.345610.4926
101.45110.14860.33480.72511.16121.60630.2287-0.5993-1.3804-0.1021-0.1437-0.02530.2028-0.12301.50190.13460.12721.21350.82682.353917.369421.043923.9411
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J

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