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- PDB-5cmk: Crystal structure of the GluK2EM LBD dimer assembly complex with ... -

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Basic information

Entry
Database: PDB / ID: 5cmk
TitleCrystal structure of the GluK2EM LBD dimer assembly complex with glutamate and LY466195
ComponentsGlutamate receptor ionotropic, kainate 2
KeywordsTRANSPORT PROTEIN / Membrane protein
Function / homology
Function and homology information


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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / neuronal action potential / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / behavioral fear response / positive regulation of synaptic transmission / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / regulation of membrane potential / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / chemical synaptic transmission / perikaryon / postsynaptic membrane / scaffold protein binding / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / ubiquitin protein ligase binding / membrane / identical protein binding / 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
GLUTAMIC ACID / : / Chem-LY5 / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsChittori, S. / Mayer, M.L.
CitationJournal: Nature / Year: 2016
Title: Structural basis of kainate subtype glutamate receptor desensitization.
Authors: Joel R Meyerson / Sagar Chittori / Alan Merk / Prashant Rao / Tae Hee Han / Mihaela Serpe / Mark L Mayer / Sriram Subramaniam /
Abstract: Glutamate receptors are ligand-gated tetrameric ion channels that mediate synaptic transmission in the central nervous system. They are instrumental in vertebrate cognition and their dysfunction ...Glutamate receptors are ligand-gated tetrameric ion channels that mediate synaptic transmission in the central nervous system. They are instrumental in vertebrate cognition and their dysfunction underlies diverse diseases. In both the resting and desensitized states of AMPA and kainate receptor subtypes, the ion channels are closed, whereas the ligand-binding domains, which are physically coupled to the channels, adopt markedly different conformations. Without an atomic model for the desensitized state, it is not possible to address a central problem in receptor gating: how the resting and desensitized receptor states both display closed ion channels, although they have major differences in the quaternary structure of the ligand-binding domain. Here, by determining the structure of the kainate receptor GluK2 subtype in its desensitized state by cryo-electron microscopy (cryo-EM) at 3.8 Å resolution, we show that desensitization is characterized by the establishment of a ring-like structure in the ligand-binding domain layer of the receptor. Formation of this 'desensitization ring' is mediated by staggered helix contacts between adjacent subunits, which leads to a pseudo-four-fold symmetric arrangement of the ligand-binding domains, illustrating subtle changes in symmetry that are important for the gating mechanism. Disruption of the desensitization ring is probably the key switch that enables restoration of the receptor to its resting state, thereby completing the gating cycle.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Oct 5, 2016Group: Database references
Revision 1.4Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)59,48410
Polymers58,7132
Non-polymers7708
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-56 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.759, 102.759, 281.992
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor ionotropic, kainate 2 / GluK2 / Glutamate receptor 6 / GluR6


Mass: 29356.621 Da / Num. of mol.: 2 / Fragment: UNP residues 429-544, 667-806 / Mutation: A487T A658S N690S F704L,A487T A658S N690S F704L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik2, Glur6 / Plasmid: PET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P42260

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Non-polymers , 6 types, 541 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-LI / LITHIUM ION / Lithium


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-LY5 / (3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid / LY466195


Mass: 346.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24F2N2O4
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Reservoir: 2M Li2SO4 3% PEG 4K 0.1M MgSO4 0.1 M NaAcetate Protein buffer: 100 mM NaCl, 5 mM LY466195, 1 mM EDTA, 10 mM HEPES pH 7 No added glutamate
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 82330 / % possible obs: 100 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 48.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G3F

3g3f


Resolution: 1.801→29.864 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 17.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1869 4135 5.04 %Random selection
Rwork0.1636 ---
obs0.1648 82330 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→29.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 48 533 4611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144252
X-RAY DIFFRACTIONf_angle_d1.4035750
X-RAY DIFFRACTIONf_dihedral_angle_d13.7971623
X-RAY DIFFRACTIONf_chiral_restr0.068638
X-RAY DIFFRACTIONf_plane_restr0.007727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8006-1.82110.2482600.23284753X-RAY DIFFRACTION98
1.8211-1.84250.24952560.22574839X-RAY DIFFRACTION99
1.8425-1.8650.21932370.21154929X-RAY DIFFRACTION100
1.865-1.88860.21562320.20024878X-RAY DIFFRACTION100
1.8886-1.91340.23832460.20254891X-RAY DIFFRACTION100
1.9134-1.93960.22042840.19054917X-RAY DIFFRACTION100
1.9396-1.96730.18842450.18424828X-RAY DIFFRACTION100
1.9673-1.99670.20882480.18214917X-RAY DIFFRACTION100
1.9967-2.02790.17862670.18114881X-RAY DIFFRACTION100
2.0279-2.06110.22292570.16964864X-RAY DIFFRACTION100
2.0611-2.09660.18932410.16944927X-RAY DIFFRACTION100
2.0966-2.13480.17042400.16714856X-RAY DIFFRACTION100
2.1348-2.17580.1782430.16594935X-RAY DIFFRACTION100
2.1758-2.22020.20592600.1624846X-RAY DIFFRACTION100
2.2202-2.26850.17642570.15944895X-RAY DIFFRACTION100
2.2685-2.32120.1742470.15534863X-RAY DIFFRACTION100
2.3212-2.37920.19732460.1674904X-RAY DIFFRACTION100
2.3792-2.44350.21482210.17324944X-RAY DIFFRACTION100
2.4435-2.51540.19882690.16864864X-RAY DIFFRACTION100
2.5154-2.59660.19012820.16154830X-RAY DIFFRACTION100
2.5966-2.68930.20292790.16994877X-RAY DIFFRACTION100
2.6893-2.79690.21452770.17764849X-RAY DIFFRACTION100
2.7969-2.92410.20872980.17094875X-RAY DIFFRACTION100
2.9241-3.07810.19882600.17244840X-RAY DIFFRACTION100
3.0781-3.27070.17042690.17124884X-RAY DIFFRACTION100
3.2707-3.52290.18673260.16214820X-RAY DIFFRACTION100
3.5229-3.87680.16872510.14274886X-RAY DIFFRACTION100
3.8768-4.43620.14612670.11894883X-RAY DIFFRACTION100
4.4362-5.58310.1552630.12874860X-RAY DIFFRACTION100
5.5831-29.86780.17762340.17464910X-RAY DIFFRACTION100
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)
10.010.0017-0.00760.00480.00010.0063-0.0117-0.01960.00850.0081-0.03560.0256-0.005-0.0123-0.00330.1326-0.0174-0.02440.1196-0.06230.129231.6944-11.575461.7468
20.0134-0.00540.00010.0166-0.0020.0004-0.01820.00270.0134-0.00910.00670.0028-0.02020.0024-0.02530.1217-0.0352-0.03670.0926-0.05740.096637.3447-9.925758.461
30.0048-0.0110.00570.0276-0.00980.0163-0.0322-0.03830.05830.0089-0.04670.0741-0.0334-0.1045-0.01280.0955-0.0044-0.02790.1984-0.13520.185917.3635-13.530958.867
40.01610.00380.01840.0063-0.00130.02730.0436-0.0439-0.0570.0448-0.00660.01040.0325-0.06760.00150.2676-0.16120.06440.3142-0.06820.212917.6194-34.570172.1558
50.00740.0026-0.00510.0009-0.00180.00350.0021-0.0069-0.00490.00420.0010.01130.004-0.0149-0.0010.2529-0.17020.08170.4532-0.08440.32028.0321-30.287668.9832
60.0721-0.0248-0.05880.0278-0.00360.0815-0.0175-0.0459-0.00060.0773-0.10640.05020.0207-0.1264-0.1240.164-0.0675-0.01450.1529-0.06220.135824.2177-27.153567.9339
70.00020.0011-00.0049-0.00030.0001-0.01950.0172-0.0084-0.00850.0048-0.0037-0.02130.0024-0.02410.1349-0.0302-0.04520.1511-0.05720.125328.0729-16.79343.9436
80.0019-0.00160.00050.0015-0.00090.00090.00920.0118-0.0162-0.00030.0018-0.00160.00510.0048-0.00070.13510.0018-0.05130.1604-0.05860.176438.1794-25.230854.3902
90.0261-0.00020.00660.0078-0.02210.06330.0047-0.03280.0196-0.0192-0.0250.0368-0.0031-0.0445-0.01790.0986-0.0225-0.05870.1423-0.040.12166.283-36.985532.6406
100.0089-0.00150.00130.00050.00180.0127-0.0162-0.01450.0259-0.0113-0.00080.022-0.019-0.0162-0.00230.10280.0252-0.05460.1928-0.08970.15846.8041-29.319533.1284
110.0297-0.0147-0.01960.09820.06610.0872-0.0181-0.04040.0013-0.05170.0103-0.0721-0.06850.0184-0.03830.0977-0.0285-0.05120.1384-0.02940.132927.6966-32.121136.6591
120.01510.0059-0.00230.0053-0.00450.00470.0082-0.00940.0202-0.01790.0104-0.0541-0.01290.01990.01010.1757-0.06620.10680.1717-0.06750.37941.2233-38.41735.4941
130.00390.00110.00460.00340.00520.0099-0.047-0.00840.0116-0.0199-0.0252-0.02920.0334-0.0031-0.00440.1801-0.02840.06620.13560.01790.199232.2563-49.943235.1454
140.1211-0.0096-0.11340.0612-0.0030.11-0.0363-0.10750.05090.0083-0.05070.0162-0.03440.0031-0.07650.1045-0.0302-0.05030.1261-0.00460.093624.1286-39.508442.9462
150.01840.0082-0.02350.0041-0.01330.0499-0.0166-0.03830.0146-0.0003-0.04510.0304-0.0204-0.0151-0.02450.1275-0.0321-0.01430.2553-0.11140.180410.0388-23.766746.9365
160.00150.0009-0.00050.0009-00.0003-0.0211-0.0159-0.0029-0.0032-0.01580.00350.0101-0.003200.1247-0.0679-0.0020.2215-0.02080.155512.1631-41.225547.1998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:21)
2X-RAY DIFFRACTION2(chain A and resid 22:53)
3X-RAY DIFFRACTION3(chain A and resid 54:109)
4X-RAY DIFFRACTION4(chain A and resid 110:145)
5X-RAY DIFFRACTION5(chain A and resid 146:166)
6X-RAY DIFFRACTION6(chain A and resid 167:226)
7X-RAY DIFFRACTION7(chain A and resid 227:240)
8X-RAY DIFFRACTION8(chain A and resid 241:253)
9X-RAY DIFFRACTION9(chain B and resid 2:40)
10X-RAY DIFFRACTION10(chain B and resid 41:60)
11X-RAY DIFFRACTION11(chain B and resid 61:137)
12X-RAY DIFFRACTION12(chain B and resid 138:171)
13X-RAY DIFFRACTION13(chain B and resid 172:190)
14X-RAY DIFFRACTION14(chain B and resid 191:225)
15X-RAY DIFFRACTION15(chain B and resid 226:242)
16X-RAY DIFFRACTION16(chain B and resid 243:254)

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