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- PDB-4bdq: Crystal structure of the GluK2 R775A LBD dimer in complex with gl... -

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Basic information

Entry
Database: PDB / ID: 4bdq
TitleCrystal structure of the GluK2 R775A 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 / inhibitory postsynaptic potential / negative regulation of synaptic transmission, glutamatergic / 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 / inhibitory postsynaptic potential / negative regulation of synaptic transmission, glutamatergic / 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 / modulation of chemical synaptic transmission / regulation of long-term neuronal synaptic plasticity / 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 / 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: 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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4206
Polymers59,0802
Non-polymers3404
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-36.6 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.753, 105.585, 114.608
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.4787, -0.8718, -0.1043), (-0.8748, -0.4837, 0.028), (-0.0749, 0.0778, -0.9942)
Vector: 25.8693, 39.2556, 42.6704)

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Components

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


Mass: 29539.830 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) / 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-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growDetails: 21% PEG 4,000, 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
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
21.54981
ReflectionResolution: 1.9→33.64 Å / Num. obs: 45850 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22.08 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 1.9 / % possible all: 99.2

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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→33.644 Å / SU ML: 0.25 / σ(F): 2 / Phase error: 19.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 2291 5 %
Rwork0.1655 --
obs0.1679 45850 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.205 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.2926 Å20 Å20 Å2
2---3.8956 Å20 Å2
3----3.397 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3975 0 22 461 4458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074075
X-RAY DIFFRACTIONf_angle_d0.9855480
X-RAY DIFFRACTIONf_dihedral_angle_d15.9331498
X-RAY DIFFRACTIONf_chiral_restr0.071613
X-RAY DIFFRACTIONf_plane_restr0.004688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94130.27121390.2442671X-RAY DIFFRACTION99
1.9413-1.98650.25271410.22072679X-RAY DIFFRACTION100
1.9865-2.03610.26371440.18482726X-RAY DIFFRACTION100
2.0361-2.09120.23151400.18082663X-RAY DIFFRACTION99
2.0912-2.15270.19411410.16872687X-RAY DIFFRACTION100
2.1527-2.22220.25541430.16892707X-RAY DIFFRACTION100
2.2222-2.30160.24271430.16992717X-RAY DIFFRACTION100
2.3016-2.39370.23031420.16782692X-RAY DIFFRACTION100
2.3937-2.50260.24851430.16672723X-RAY DIFFRACTION100
2.5026-2.63450.24281430.16962711X-RAY DIFFRACTION100
2.6345-2.79950.2261430.1722714X-RAY DIFFRACTION100
2.7995-3.01550.19871430.17152733X-RAY DIFFRACTION100
3.0155-3.31870.20371450.17272750X-RAY DIFFRACTION100
3.3187-3.79840.20681450.1562755X-RAY DIFFRACTION99
3.7984-4.78340.15921460.12682762X-RAY DIFFRACTION100
4.7834-33.64960.16911500.14292869X-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)
11.17230.905-0.09291.1121-0.20490.0865-0.25690.30890.3422-0.03590.16270.2353-0.1010.06610.0860.0834-0.0366-0.03780.1008-0.00330.210540.232131.546710.38
20.9864-0.08860.35510.9801-0.22461.2238-0.0650.0616-0.0169-0.11660.0606-0.18960.01670.12750.00650.1103-0.02060.03860.1165-0.03110.138538.66916.344710.132
32.0717-0.16290.59642.4282-0.76711.23120.00840.12880.1629-0.3408-0.01890.21680.0407-0.01720.01460.12930.0149-0.01720.13310.01180.142416.793219.67142.2945
40.82310.2035-0.16131.38190.13080.5267-0.0187-0.1778-0.01830.2221-0.0165-0.03390.05370.00710.02670.1509-0.0101-0.02550.1357-0.02270.133434.668818.964122.3919
55.6263-5.82794.90126.3319-5.02414.2790.005-0.0244-0.1641-0.3524-0.1885-0.2532-0.2779-0.22040.16040.15520.0257-0.00560.26270.02960.159427.774117.38966.13
60.85391.0616-0.38191.4473-0.36960.2474-0.0862-0.0936-0.0924-0.12130.04670.1520.0734-0.01240.04120.13720.01250.01220.08730.02140.152719.1179-10.182926.9727
71.0938-0.0782-0.26931.78530.21660.08810.0742-0.3551-0.16540.2897-0.0344-0.21180.03140.0509-0.02810.177-0.0124-0.03490.18960.03370.117531.99991.00733.9859
82.0442-0.6297-0.71741.49180.40951.3535-0.1239-0.31740.02770.16370.04460.1111-0.12750.11810.04810.16050.01990.01950.1583-0.01430.124515.900914.242840.579
90.73940.6024-0.28561.4379-0.55630.3898-0.10490.0303-0.0216-0.26120.1366-0.02980.0283-0.0039-0.01310.14980.0005-0.00320.1087-0.00280.119424.07090.369518.4973
104.6180.554-3.65042.46670.7833.5066-0.2809-1.06080.32910.4940.3986-0.2543-0.5963-0.2835-0.15060.22170.07770.03380.234-0.02520.128322.94056.098635.5506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 431:458)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 459:535)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 536:763)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 764:800)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 900)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 431:484)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 485:535)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 536:763)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 764:800)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 900)

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