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

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Open data


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Basic information

Entry
Database: PDB / ID: 4bdn
TitleCrystal structure of the GluK2 K531A-T779G LBD dimer in complex with glutamate
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 / glutamate receptor activity / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / regulation of JNK cascade ...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 / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / 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 / 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: 2.5 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 1.2Apr 29, 2015Group: Data collection
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_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_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 1.4Nov 13, 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 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)118,77612
Polymers118,0954
Non-polymers6808
Water6,071337
1
A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3886
Polymers59,0482
Non-polymers3404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-36.7 kcal/mol
Surface area22330 Å2
MethodPISA
2
C: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
D: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3886
Polymers59,0482
Non-polymers3404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-34.6 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.729, 100.133, 126.199
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(-0.983, -0.1786, -0.0432), (-0.1669, 0.7701, 0.6157), (-0.0767, 0.6124, -0.7868)-24.6489, -7.1795, 13.941
2given(-0.9959, 0.0057, -0.0906), (-0.0021, -0.9992, -0.0398), (-0.0907, -0.0394, 0.9951)-65.3261, -0.1379, -2.7279
3given(0.9866, 0.1568, 0.0452), (0.0928, -0.767, 0.6349), (0.1342, -0.6222, -0.7713)40.0177, 1.0354, 20.4289

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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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 25% PEG 4,000, 6% PROPAN-2-OL, 80MM NA ACETATE

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONBESSY 14.210.91841
SYNCHROTRONDiamond I0221.5498
Detector
TypeIDDetector
MARRESEARCH1CCD
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
21.54981
ReflectionResolution: 2.5→32.56 Å / Num. obs: 38135 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 31.27 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / % 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 2XXR

2xxr


Resolution: 2.5→32.561 Å / SU ML: 0.35 / σ(F): 1.99 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1908 5 %
Rwork0.1975 --
obs0.2001 38135 99.66 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.025 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4001 Å20 Å20 Å2
2---1.3568 Å20 Å2
3---2.7569 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7902 0 44 337 8283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068362
X-RAY DIFFRACTIONf_angle_d0.72110887
X-RAY DIFFRACTIONf_dihedral_angle_d11.6613023
X-RAY DIFFRACTIONf_chiral_restr0.0521210
X-RAY DIFFRACTIONf_plane_restr0.0031371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.29221350.25012552X-RAY DIFFRACTION100
2.5625-2.63180.31991350.24982570X-RAY DIFFRACTION100
2.6318-2.70920.32181340.26362539X-RAY DIFFRACTION100
2.7092-2.79660.31941340.24782561X-RAY DIFFRACTION100
2.7966-2.89650.2931350.2452553X-RAY DIFFRACTION100
2.8965-3.01230.2771350.22242569X-RAY DIFFRACTION100
3.0123-3.14930.27941360.21692583X-RAY DIFFRACTION100
3.1493-3.31520.27851350.21122568X-RAY DIFFRACTION100
3.3152-3.52270.27451350.21022558X-RAY DIFFRACTION100
3.5227-3.79430.24971360.20082585X-RAY DIFFRACTION100
3.7943-4.17540.22091360.17112595X-RAY DIFFRACTION100
4.1754-4.7780.19251380.13732623X-RAY DIFFRACTION100
4.778-6.01360.18131390.1652637X-RAY DIFFRACTION99
6.0136-32.56380.22141450.18152734X-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)
10.31590.4590.00020.6704-0.11122.6454-0.0156-0.04470.11550.0564-0.05320.19730.1988-0.32840.05240.0304-0.02450.03430.072-0.00490.0792-26.9116-9.230723.9607
20.35810.0703-0.30410.3483-0.29981.04630.0423-0.1-0.0315-0.0568-0.11270.00130.03020.27320.05340.0445-0.0344-0.00250.12470.01760.0466-7.5194-3.08122.8235
31.17631.082-0.96071.4346-0.5962.20170.2179-0.4126-0.12980.2848-0.2812-0.1556-0.23450.70890.05070.0767-0.055-0.01240.23860.0003-0.0221-3.60564.674931.2152
40.29390.96680.50413.14771.63311.6537-0.11190.06210.13030.0934-0.03870.47260.02870.160.1470.0296-0.02150.0050.09640.0130.0762-13.95562.667520.5149
50.7818-0.10520.08952.41922.85893.7059-0.2307-0.0737-0.1445-0.23930.1020.4137-0.28850.34720.12080.0461-0.0178-0.04970.05610.05860.1348-25.25931.145112.3251
627.85296.2147229.6622-0.0174-0.0781-0.08250.28-0.1576-0.0646-0.22010.18240.17410.22-0.0796-0.06080.10460.0940.0482-9.6852-1.314924.6039
70.63860.7253-0.37290.8241-0.39231.11420.0267-0.0654-0.1372-0.0426-0.0088-0.1742-0.1270.44860.00320.0869-0.04880.04130.21280.00440.13421.65397.2964-9.7505
81.31390.0452-0.25080.4201-0.3390.3094-0.00680.1969-0.0683-0.0674-0.00470.03110.1114-0.03030.00440.07140.01380.01120.1243-0.01430.0217-11.4031-1.8451-7.4864
91.71420.815-0.91590.7188-1.01161.48730.1360.2370.61450.05290.21610.2787-0.0688-0.2203-0.34620.1112-0.07820.0670.01770.20930.192-24.1817.807-5.3111
101.19350.8115-0.3930.6135-0.12170.4911-0.1225-0.0896-0.0298-0.04090.16390.0084-0.05640.2719-0.03470.0929-0.0506-0.01540.1120.02070.1155-10.8346.60121.4011
112.2736-1.46520.19332.0838-1.31332.1732-0.0275-0.2882-0.43360.09960.17380.1375-0.22340.3694-0.14160.0196-0.09930.03180.1838-0.01580.14530.239810.23416.4112
1222-7.5567225.3905-0.02270.0131-0.0394-0.0948-0.0540.0436-0.1005-0.02770.07520.55050.17460.12570.19670.09230.0585-16.39358.48-5.5075
130.6881-0.64410.3340.7247-0.0480.8057-0.0609-0.0639-0.06810.12890.1050.144-0.1971-0.077-0.03370.08790.0375-0.01370.07230.02520.2129-44.6768.998723.5339
140.86950.274-0.21210.4082-0.31610.35120.00740.10520.3070.04330.12740.1759-0.0348-0.2148-0.1414-0.03380.0833-0.05740.05570.12540.2365-58.9018-0.5419.5397
150.53870.2548-0.39431.5850.18541.72690.19350.03510.14140.14820.03220.0716-0.0849-0.5518-0.22060.04670.04810.01740.20860.06920.1157-64.5783-5.828327.8899
160.12650.581-0.30222.6211-1.41070.7616-0.16660.1173-0.10480.36920.2443-0.4013-0.1952-0.3356-0.07640.090.0466-0.1420.17230.1130.2399-53.5321-2.836317.9546
172.03621.7824-0.73191.9413-1.39831.7912-0.22190.1451-0.1728-0.17360.2279-0.18980.1844-0.1628-0.00850.0607-0.0018-0.02160.04260.02840.2271-41.3755-1.624111.227
18222222-0.46230.14240.30560.3420.60610.111-0.1085-0.2957-0.14480.21820.05160.01590.30710.06550.3217-58.13780.55722.4281
190.61640.52330.11940.45530.09150.0283-0.28070.46490.4464-0.24690.42810.4120.0081-0.1958-0.12370.0014-0.2517-0.44580.39470.35850.2549-60.5869-3.0086-12.4214
201.10580.6424-0.11240.4060.00070.1222-0.19470.27160.2011-0.04120.16490.02580.1196-0.07110.00840.1064-0.0913-0.11250.14330.1130.077-48.513-6.5193-4.4589
211.15530.2762-0.21881.0788-0.2010.0641-0.15880.42340.0137-0.3380.2592-0.09140.05520.0277-0.06590.0055-0.1915-0.10240.0528-0.1295-0.1169-39.8553-16.4266-7.9709
220.87511.5311-0.39263.3539-0.66930.1724-0.27170.20420.1666-0.20990.31370.35080.1272-0.1494-0.04280.1843-0.1289-0.09270.10410.05590.0861-53.3285-12.2851-1.6702
232.7059-0.38782.05270.4405-0.11151.6415-0.3187-0.01420.82540.03890.15340.2296-0.0163-0.37240.14140.0163-0.0559-0.03370.24870.16010.4081-65.1542-4.52233.345
249.1602-6.54040.632220.29774.3293-0.04430.220.04610.00180.0012-0.02170.2643-0.35790.04230.1448-0.1433-0.04430.21020.04620.0366-48.5955-8.6099-7.0939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 431:483)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 484:677)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 678:746)
4X-RAY DIFFRACTION4(CHAIN A AND (RESID 747:775 OR RESID 803:804))
5X-RAY DIFFRACTION5(CHAIN A AND RESID 776:801)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 900)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 431:469)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 470:535)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 536:747)
10X-RAY DIFFRACTION10(CHAIN B AND (RESID 748:783 OR RESID 803:804))
11X-RAY DIFFRACTION11(CHAIN B AND RESID 784:801)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 900)
13X-RAY DIFFRACTION13(CHAIN C AND RESID 431:499)
14X-RAY DIFFRACTION14(CHAIN C AND RESID 500:678)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 679:746)
16X-RAY DIFFRACTION16(CHAIN C AND (RESID 747:775 OR RESID 803:804))
17X-RAY DIFFRACTION17(CHAIN C AND RESID 776:801)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 900)
19X-RAY DIFFRACTION19(CHAIN D AND RESID 432:498)
20X-RAY DIFFRACTION20(CHAIN D AND RESID 499:675)
21X-RAY DIFFRACTION21(CHAIN D AND RESID 676:742)
22X-RAY DIFFRACTION22(CHAIN D AND (RESID 743:774 OR RESID 803:804))
23X-RAY DIFFRACTION23(CHAIN D AND RESID 775:801)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 900)

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