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- PDB-2xxt: Crystal structure of the GluK2 (GluR6) wild-type LBD dimer in com... -

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Basic information

Entry
Database: PDB / ID: 2xxt
TitleCrystal structure of the GluK2 (GluR6) wild-type LBD dimer in complex with kainate
ComponentsGLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
KeywordsTRANSPORT 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 / regulation of JNK cascade / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / neuronal action potential / behavioral fear response / positive regulation of synaptic transmission / 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 / regulation of membrane potential / SNARE binding / excitatory postsynaptic potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / 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 / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic density / axon / neuronal cell body / glutamatergic synapse / ubiquitin protein ligase binding / dendrite / synapse / identical protein binding / membrane / 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
3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNayeem, N. / Mayans, O. / Green, T.
CitationJournal: J.Neurosci. / Year: 2011
Title: Conformational Flexibility of the Ligand-Binding Domain Dimer in Kainate Receptor Gating and Desensitization
Authors: Nayeem, N. / Mayans, O. / Green, T.
History
DepositionNov 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_conn.ptnr2_label_seq_id / _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 2
B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7607
Polymers59,2522
Non-polymers5085
Water7,512417
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-45 kcal/mol
Surface area22490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.285, 105.915, 113.478
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2 / GLUTAMATE RECEPTOR 6 / GLUR-6 / GLUR6


Mass: 29625.943 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 429-544,667-806
Source method: isolated from a genetically manipulated source
Details: GLY-THR LINKER / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42260
#2: Chemical ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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.: 417 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS FUSION OF TWO SEQUENCE RANGES JOINED BY ARTIFICIAL 2 RESIDUE LINKER.

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION, HANGING DROP 23% PEG 4000, 9% PROPAN-2-OL, 80MM SODIUM ACETATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→19.7 Å / Num. obs: 44830 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.8 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XXR

2xxr


Resolution: 1.9→19.724 Å / SU ML: 0.24 / σ(F): 2.01 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 2242 5 %
Rwork0.1722 --
obs0.1741 44830 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.765 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6412 Å20 Å20 Å2
2---4.2127 Å20 Å2
3----0.4285 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 0 33 417 4414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074084
X-RAY DIFFRACTIONf_angle_d1.0565500
X-RAY DIFFRACTIONf_dihedral_angle_d15.8031514
X-RAY DIFFRACTIONf_chiral_restr0.076618
X-RAY DIFFRACTIONf_plane_restr0.004689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94130.26431400.23142671X-RAY DIFFRACTION99
1.9413-1.98640.24371430.20782700X-RAY DIFFRACTION99
1.9864-2.0360.23171410.18462696X-RAY DIFFRACTION99
2.036-2.0910.21911420.17682690X-RAY DIFFRACTION99
2.091-2.15250.20421400.16952663X-RAY DIFFRACTION98
2.1525-2.22190.22411410.1622684X-RAY DIFFRACTION98
2.2219-2.30120.21171410.17482678X-RAY DIFFRACTION98
2.3012-2.39310.22271400.16322653X-RAY DIFFRACTION97
2.3931-2.50190.19121400.1652660X-RAY DIFFRACTION97
2.5019-2.63350.20981400.16112649X-RAY DIFFRACTION97
2.6335-2.7980.2031390.17512647X-RAY DIFFRACTION96
2.798-3.01340.21141390.18482644X-RAY DIFFRACTION96
3.0134-3.31530.22971380.17562625X-RAY DIFFRACTION95
3.3153-3.79210.19791380.17012626X-RAY DIFFRACTION94
3.7921-4.76650.16391390.13542631X-RAY DIFFRACTION94
4.7665-19.72490.20451410.16152671X-RAY DIFFRACTION92
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)
11.6031-1.21640.66091.5391-0.16531.4976-0.218-0.08450.2272-0.04660.07160.0248-0.3696-0.28280.11310.17860.0452-0.0310.19270.01560.21136.7708-25.0967-14.0605
20.6692-0.29980.75991.4174-0.31551.46870.02270.0344-0.08470.17570.0390.0301-0.0181-0.1095-0.04670.15580.01340.0080.15240.01990.148519.1878-38.921-5.9328
32.9441-0.12540.48981.12280.07952.4621-0.0002-0.2420.37320.3266-0.0369-0.1419-0.1549-0.03610.04270.1813-0.0186-0.00960.148-0.00340.14930.0109-33.6651-1.5693
41.0318-1.0902-0.46791.65920.15071.73960.08660.1264-0.0718-0.1902-0.16510.06130.15260.08410.0620.10640.0042-0.03740.11790.00750.115813.1321-35.3695-22.2541
50.6966-1.15630.25735.76040.98852.89020.14970.2182-0.1044-0.066-0.48250.30380.0096-0.10710.32960.1275-0.018-0.01240.2444-0.02360.165220.2292-35.0119-5.7383
61.18-1.6817-0.34582.68660.47080.5297-0.19920.0147-0.11740.14920.1455-0.1860.26940.06380.03850.1523-0.0332-0.00920.0739-0.02280.150529.5185-63.3912-26.428
71.00290.0384-0.15920.8469-0.25841.0768-0.05010.15740.0295-0.30120.04280.1754-0.0647-0.22520.0090.2022-0.0131-0.04850.1888-0.0160.131622.3792-46.5658-35.2142
82.75550.8691-1.41012.5711-0.01472.6785-0.00430.3292-0.1005-0.3937-0.0085-0.1903-0.3189-0.10060.01260.23430.00130.00460.181-0.00270.127231.7555-39.4963-40.5163
91.3692-0.8581-0.262.19430.48270.8694-0.0742-0.2021-0.04310.23210.06810.0690.012-0.07550.01250.15660.0038-0.00670.16770.00730.129723.9329-52.6657-18.6887
102.28621.0112.98070.57451.51594.4299-0.2261-0.3393-0.1456-0.2308-0.06620.106-0.3579-0.47690.22790.2715-0.05310.02710.2227-0.04080.16226.2283-47.347-35.6767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 429:483)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 484:677)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 678:762)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 763:805)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 900)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 429:483)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 484:677)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 678:762)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 763:805)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 900)

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