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- PDB-2xxu: Crystal structure of the GluK2 (GluR6) M770K LBD dimer in complex... -

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Basic information

Entry
Database: PDB / ID: 2xxu
TitleCrystal structure of the GluK2 (GluR6) M770K LBD dimer in complex with glutamate
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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / regulation of JNK cascade / glutamate receptor activity ...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 / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / regulation of JNK cascade / glutamate receptor activity / ubiquitin conjugating enzyme binding / receptor clustering / modulation of excitatory postsynaptic potential / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / behavioral fear response / positive regulation of synaptic transmission / 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 / dendrite cytoplasm / presynaptic modulation of chemical synaptic transmission / SNARE binding / hippocampal mossy fiber to CA3 synapse / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / excitatory postsynaptic potential / regulation of membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / presynaptic membrane / scaffold protein binding / perikaryon / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / ubiquitin protein ligase binding / dendrite / synapse / glutamatergic 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
GLUTAMIC ACID / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)59,6247
Polymers59,2482
Non-polymers3765
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-42.3 kcal/mol
Surface area22050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.266, 104.781, 114.204
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: 29623.928 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 429-544,667-806 / Mutation: YES
Source method: isolated from a genetically manipulated source
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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 770 TO LYS ENGINEERED RESIDUE IN CHAIN B, MET 770 TO LYS

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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: 2.45 Å3/Da / Density % sol: 50 %
Description: THE LONGER WAVELENGTH WAS USED TO LOCATE THE CHLORIDE IONS IN THIS STRUCTURE AND WAS NOT USED FOR STRUCTURE DETERMINATION.
Crystal growMethod: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION, HANGING DROP. 27% 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: I02 / Wavelength: 0.9795, 1.5498
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.54981
ReflectionResolution: 1.5→19.9 Å / Num. obs: 87370 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 17.72 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.9
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / % possible all: 96.6

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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: 1.5→19.898 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 17.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1891 4369 5 %
Rwork0.1694 --
obs0.1704 87370 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.953 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9334 Å2-0 Å2-0 Å2
2---2.4539 Å20 Å2
3----0.4795 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 23 492 4503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064098
X-RAY DIFFRACTIONf_angle_d1.0365512
X-RAY DIFFRACTIONf_dihedral_angle_d15.8821522
X-RAY DIFFRACTIONf_chiral_restr0.07614
X-RAY DIFFRACTIONf_plane_restr0.004692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.33551470.25712789X-RAY DIFFRACTION97
1.5171-1.53490.25171450.23782753X-RAY DIFFRACTION97
1.5349-1.55360.22711440.22152749X-RAY DIFFRACTION96
1.5536-1.57330.22051460.21842761X-RAY DIFFRACTION97
1.5733-1.5940.23321470.20782790X-RAY DIFFRACTION96
1.594-1.61580.23251430.20472722X-RAY DIFFRACTION96
1.6158-1.63890.23031440.19272745X-RAY DIFFRACTION96
1.6389-1.66330.2161440.18872732X-RAY DIFFRACTION96
1.6633-1.68930.18651460.18522765X-RAY DIFFRACTION96
1.6893-1.7170.20031430.17442733X-RAY DIFFRACTION96
1.717-1.74660.20431440.17292737X-RAY DIFFRACTION95
1.7466-1.77830.18481440.16662721X-RAY DIFFRACTION95
1.7783-1.81250.2081430.1642727X-RAY DIFFRACTION95
1.8125-1.84940.19771440.16242725X-RAY DIFFRACTION95
1.8494-1.88960.1911430.15922728X-RAY DIFFRACTION94
1.8896-1.93350.19941440.1662731X-RAY DIFFRACTION94
1.9335-1.98190.17861360.17462593X-RAY DIFFRACTION91
1.9819-2.03540.19641460.16052768X-RAY DIFFRACTION96
2.0354-2.09520.17551490.14932831X-RAY DIFFRACTION98
2.0952-2.16280.19931490.15452826X-RAY DIFFRACTION98
2.1628-2.240.20321470.15582803X-RAY DIFFRACTION98
2.24-2.32950.18181500.15312845X-RAY DIFFRACTION97
2.3295-2.43540.17591480.15962803X-RAY DIFFRACTION97
2.4354-2.56350.17411480.16222815X-RAY DIFFRACTION97
2.5635-2.72380.17791490.15842830X-RAY DIFFRACTION97
2.7238-2.93350.1771470.1712801X-RAY DIFFRACTION96
2.9335-3.22750.18481480.17022803X-RAY DIFFRACTION96
3.2275-3.6920.17211470.16612790X-RAY DIFFRACTION95
3.692-4.64170.15521460.14482789X-RAY DIFFRACTION94
4.6417-19.89990.19571480.17432796X-RAY DIFFRACTION91
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)
11.0030.56570.18361.0662-0.19270.7841-0.06830.0833-0.1894-0.05980.01420.00270.2238-0.0562-00.1286-0.02790.02240.12150.01320.1679-41.028824.256813.7955
21.40220.1089-0.58731.35590.10151.374-0.05690.03910.0546-0.14180.0450.0046-0.0047-0.038900.1147-0.0224-0.01080.09030.030.0881-28.818838.13155.6939
32.31640.0508-0.5961.92150.70481.3044-0.00270.179-0.2279-0.2607-0.0017-0.0855-0.041-0.04-0.00010.13070.00410.01270.1233-0.00890.1159-18.53732.90741.6569
40.57810.68320.31070.8430.1740.50810.0478-0.1192-0.00540.1617-0.09440.040.0044-0.0252-0.00030.1244-0.0110.02740.12430.02150.1231-35.012534.717521.9505
57.4527-5.3078-1.71374.76613.34014.9493-0.0054-0.04810.0485-0.0074-0.01040.0864-0.0005-0.0632-0.030.11810.01920.00560.16660.00970.1601-27.704235.00576.0279
60.87670.7101-0.00811.4290.47880.4601-0.0815-0.10920.1563-0.10940.0604-0.0475-0.0714-0.014300.15250.0147-0.02160.1198-0.02060.1504-19.144962.671326.4791
71.5568-0.09730.43330.95-0.45330.87480.0191-0.2367-0.060.1123-0.01470.12440.0199-0.1335-0.00010.1488-0.010.02060.1649-0.00370.0969-25.936446.017835.5572
81.7029-0.63870.52891.2988-0.2641.5148-0.0836-0.2965-0.05870.1650.0416-0.10060.0016-0.16330.00010.15740.0164-0.02210.17730.02430.133-16.763239.770440.9683
90.92260.85030.48721.34530.48430.5284-0.07130.0998-0.0216-0.18630.0856-0.0497-0.03010.0443-0.00020.14160.0086-0.00190.12510.00710.1072-23.672751.864118.93
102.35741.72332.00442.22131.95042.2693-0.0879-0.3404-0.19080.239-0.04340.1286-0.0804-0.1852-0.14210.21720.0496-0.01790.1850.01880.1536-22.809146.359635.4363
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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