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- PDB-4bdo: Crystal structure of the GluK2 K531A-T779G LBD dimer in complex w... -

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Basic information

Entry
Database: PDB / ID: 4bdo
TitleCrystal structure of the GluK2 K531A-T779G LBD dimer in complex with kainate
ComponentsGLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
KeywordsMETAL TRANSPORT / IONOTROPIC GLUTAMATE RECEPTOR / KAINATE RECEPTOR
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 / 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding / regulation of JNK cascade / 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 / 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 / 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 / neuron apoptotic process / chemical synaptic transmission / perikaryon / negative regulation of neuron apoptotic process / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / synapse / dendrite / ubiquitin protein ligase binding / 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 / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / Glutamate receptor ionotropic, kainate 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsNayeem, N. / Mayans, O. / Green, T.
CitationJournal: Open Biol. / Year: 2013
Title: Correlating Efficacy and Desensitization with Gluk2 Ligand-Binding Domain Movements.
Authors: Nayeem, N. / Mayans, O. / Green, T.
History
DepositionOct 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Dec 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
D: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,18713
Polymers118,0954
Non-polymers1,0929
Water2,774154
1
A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5206
Polymers59,0482
Non-polymers4724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-34.9 kcal/mol
Surface area21430 Å2
MethodPISA
2
C: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
D: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6677
Polymers59,0482
Non-polymers6205
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-34.3 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.838, 99.819, 124.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9947, -0.0942, 0.0416), (-0.1008, 0.8077, -0.5809), (0.0211, -0.582, -0.8129)64.1049, 6.9441, 11.181
2given(-0.9958, 0.0107, -0.0914), (-0.0077, -0.9994, -0.0324), (-0.0917, -0.0315, 0.9953)105.8793, 0.4079, 4.7812
3given(0.9849, 0.1129, 0.1309), (0.1677, -0.8074, -0.5656), (0.0419, 0.5791, -0.8142)-40.5954, -7.7137, 10.296

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Components

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


Mass: 29523.787 Da / Num. of mol.: 4 / 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) / 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.: 4 / Source method: obtained synthetically / Formula: C10H15NO4 / Comment: neurotransmitter, agonist*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE (KAI): D 900 IS KAI FOR ALT CONF A AND GLU FOR ALT CONF B ...3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE (KAI): D 900 IS KAI FOR ALT CONF A AND GLU FOR ALT CONF B GLUTAMIC ACID (GLU): IS PRESENT AS ALT CONF B FOR RESIDUE 900.

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growDetails: 27% PEG 4,000, 6% PROPAN-2-OL, 80MM NA ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.95
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.55→40.79 Å / Num. obs: 35522 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 42.34 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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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 2XXT

2xxt


Resolution: 2.55→40.785 Å / SU ML: 0.37 / σ(F): 1.99 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2407 1777 5 %
Rwork0.1913 --
obs0.1938 35522 99.54 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.456 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.8664 Å20 Å20 Å2
2---1.5651 Å20 Å2
3---10.4315 Å2
Refinement stepCycle: LAST / Resolution: 2.55→40.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7749 0 74 154 7977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088229
X-RAY DIFFRACTIONf_angle_d0.88610722
X-RAY DIFFRACTIONf_dihedral_angle_d13.7332973
X-RAY DIFFRACTIONf_chiral_restr0.0621206
X-RAY DIFFRACTIONf_plane_restr0.0031339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.6190.41261350.30692557X-RAY DIFFRACTION100
2.619-2.6960.35831340.27922545X-RAY DIFFRACTION99
2.696-2.7830.33931350.26452570X-RAY DIFFRACTION100
2.783-2.88240.331350.25162571X-RAY DIFFRACTION100
2.8824-2.99780.30921350.22732562X-RAY DIFFRACTION100
2.9978-3.13420.26851370.21272601X-RAY DIFFRACTION100
3.1342-3.29940.27261360.19922587X-RAY DIFFRACTION100
3.2994-3.5060.24471350.19752553X-RAY DIFFRACTION99
3.506-3.77650.21721370.17822602X-RAY DIFFRACTION100
3.7765-4.15620.18561360.15932602X-RAY DIFFRACTION100
4.1562-4.75690.19921390.13522630X-RAY DIFFRACTION100
4.7569-5.99010.19411390.17242643X-RAY DIFFRACTION99
5.9901-40.78980.21351440.18382722X-RAY DIFFRACTION98
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)
13.3240.8278-0.55940.959-0.84221.9589-0.0163-0.45390.33290.11160.0830.2253-0.3131-0.1236-0.04860.14190.0356-0.04430.1549-0.00750.28933.29363.914121.7478
20.3016-0.553-0.1692.0837-0.54963.79530.172-0.5270.43180.14420.22160.6645-0.1488-1.0771-0.23730.09450.0710.1440.50930.0920.384418.0076-4.016726.9043
32.8320.61460.8982.3861-1.39941.5368-0.1423-0.1955-0.17840.09930.2381-0.5040.0993-0.4226-0.12090.16090.0232-0.01420.31350.07060.24830.5317-7.030623.291
41.53780.0865-0.76012.2206-0.80150.7835-0.17280.29-0.1683-0.40550.1742-0.32790.29150.08250.12340.1040.0071-0.09340.2010.03140.241543.7386-0.314511.4062
54.0121.24711.87161.0392-1.15925.9969-0.02840.065-0.0179-0.03660.19170.03860.14620.0457-0.19720.4344-0.10780.03810.43060.0670.326628.07490.573423.2899
62.7018-0.05590.26261.915-0.76521.5439-0.06780.3711-0.0107-0.23460.21890.33280.1075-0.1374-0.17080.2212-0.1034-0.15990.2520.09850.261631.0672-4.6251-8.22
72.1098-0.3208-0.38111.9554-1.19640.9178-0.11950.46580.0778-0.43760.0206-0.22610.09940.21040.07420.2525-0.0552-0.01020.2706-0.08540.202145.7253-16.1208-7.9776
80.3106-0.4975-0.4913.33140.70620.6991-0.18290.0228-0.03530.12220.23050.6080.10810.0012-0.14370.3414-0.0848-0.19070.25360.0510.347632.9777-13.2091-1.416
90.6175-0.72780.58462.1372-0.62641.0565-0.3621-0.13490.18170.0310.51690.22920.192-0.4641-0.08750.1377-0.0793-0.07480.32430.13530.423320.8064-3.94793.1121
102.1028-0.0651-0.72451.8112.38883.5558-0.07240.19610.0896-0.08680.17050.06530.6447-0.3243-0.04670.49250.0198-0.03340.56880.04070.272736.5589-8.9596-7.574
111.6538-0.12030.5992.24930.13991.2324-0.2027-0.43960.0320.16740.2347-0.11940.11570.0072-0.0350.14950.0530.00990.2663-0.03960.132171.3562-4.819223.6636
120.5326-0.97381.02715.08930.08863.5784-0.3155-0.380.28730.46020.4668-1.3937-0.25741.1565-0.04030.29460.1041-0.25930.4888-0.17340.330484.43113.747231.287
130.30540.44410.43414.69313.20272.814-0.2748-0.24570.21370.081-0.10080.9842-0.1385-0.14360.25410.22380.04360.00350.2962-0.07460.280772.04335.134122.9564
140.6450.4195-0.43642.41571.38892.2179-0.1285-0.27920.011-0.16430.20050.1891-0.32710.39030.0040.11050.0152-0.01140.2444-0.03080.282761.1468-0.205112.2672
155.08932.69992.46371.94092.59134.4377-0.18780.1678-0.0139-0.5048-0.0864-0.05530.0692-0.07160.29780.44320.01120.16640.6208-0.04740.213475.4707-1.542725.4174
161.89260.20030.28381.1549-0.19131.86030.03820.29540.3607-0.1444-0.0119-0.03710.18480.1609-0.0140.2092-0.03860.06130.20040.03490.186575.97234.8871-5.8859
171.77940.1320.00012.2718-0.05011.45460.0220.31540.5378-0.17610.20630.0885-0.2235-0.0857-0.18490.3017-0.05810.00820.19250.11390.363863.093316.9324-5.5541
182.8818-1.24650.17581.8208-0.58191.21310.1933-0.59220.1223-0.2599-0.08090.08550.1018-0.0088-0.04480.13030.05240.09280.2240.06580.317779.7439-5.48982.522
191.30120.7749-1.14973.5032-0.42652.2083-0.1126-0.44780.37810.18060.19870.3134-0.43310.7604-0.18260.2161-0.0580.07370.3708-0.07210.465385.781210.66686.3002
200.20660.4138-0.10181.0413-0.29310.08770.012-0.0808-0.0039-0.00890.0766-0.0367-0.04350.1331-0.04720.86550.2050.35640.36260.13440.519869.60548.5731-5.9465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 431:683)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 684:728)
3X-RAY DIFFRACTION3(CHAIN A AND (RESID 729:773 OR RESID 804))
4X-RAY DIFFRACTION4(CHAIN A AND RESID 774:800)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 900)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 431:677)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 678:742)
8X-RAY DIFFRACTION8(CHAIN B AND (RESID 743:773 OR RESID 804))
9X-RAY DIFFRACTION9(CHAIN B AND RESID 774:800)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 900)
11X-RAY DIFFRACTION11(CHAIN C AND RESID 431:684)
12X-RAY DIFFRACTION12(CHAIN C AND RESID 685:736)
13X-RAY DIFFRACTION13(CHAIN C AND (RESID 737:773 OR RESID 804))
14X-RAY DIFFRACTION14(CHAIN C AND RESID 774:800)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 900)
16X-RAY DIFFRACTION16(CHAIN D AND RESID 431:677)
17X-RAY DIFFRACTION17(CHAIN D AND (RESID 678:762 OR RESID 804))
18X-RAY DIFFRACTION18(CHAIN D AND RESID 763:785)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 786:800)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 900)

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