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- PDB-4z0i: Crystal structure of a tetramer of GluA2 ligand binding domains b... -

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Basic information

Entry
Database: PDB / ID: 4z0i
TitleCrystal structure of a tetramer of GluA2 ligand binding domains bound with glutamate at 1.45 Angstrom resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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 / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsBaranovic, J. / Chebli, M. / Salazar, H. / Carbone, A.L. / Ghisi, V. / Faelber, K. / Lau, A.Y. / Daumke, O. / Plested, A.J.R.
CitationJournal: To Be Published
Title: Crystal structure of the tetrameric wt GluA2 ligand-binding domain bound to glutamate at 1.45 Angstroms resolution
Authors: Baranovic, J. / Chebli, M. / Salazar, H. / Carbone, A.L. / Ghisi, V. / Faelber, K. / Lau, A.Y. / Daumke, O. / Plested, A.J.R.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 2.0Mar 25, 2020Group: Atomic model / Derived calculations
Category: atom_site / pdbx_struct_assembly ...atom_site / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _atom_site.occupancy
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,60812
Polymers58,4432
Non-polymers1,16410
Water15,313850
1
A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,90814
Polymers58,4432
Non-polymers1,46512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+1,y,-z-11
Buried area3600 Å2
ΔGint-24 kcal/mol
Surface area24890 Å2
MethodPISA
2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,30710
Polymers58,4432
Non-polymers8648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_553-x,y,-z-21
Buried area2630 Å2
ΔGint-33 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.190, 47.270, 116.820
Angle α, β, γ (deg.)90.00, 93.57, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-599-

HOH

21A-683-

HOH

31B-694-

HOH

41B-792-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate receptor 2,Glutamate receptor 2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / ...GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 29221.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Variant (production host): Origami B / References: UniProt: P19491

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Non-polymers , 5 types, 860 molecules

#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 850 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.72 % / Description: Cube-like crystals
Crystal growTemperature: 277.14 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350 and 200 mM KNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 26, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 90541 / Num. obs: 90541 / % possible obs: 99 % / Redundancy: 4.1 % / Rsym value: 0.075 / Net I/σ(I): 11.7
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 1.45→47.27 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 19.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 4607 5.09 %random selection
Rwork0.1772 ---
obs0.1788 90525 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4084 0 70 850 5004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084366
X-RAY DIFFRACTIONf_angle_d1.195900
X-RAY DIFFRACTIONf_dihedral_angle_d12.1181684
X-RAY DIFFRACTIONf_chiral_restr0.079646
X-RAY DIFFRACTIONf_plane_restr0.006740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46650.24611610.22532834X-RAY DIFFRACTION98
1.4665-1.48370.2861460.21482844X-RAY DIFFRACTION98
1.4837-1.50180.2681330.20992798X-RAY DIFFRACTION99
1.5018-1.52080.26111400.20482904X-RAY DIFFRACTION98
1.5208-1.54090.24421380.19532780X-RAY DIFFRACTION99
1.5409-1.5620.21521560.18612878X-RAY DIFFRACTION99
1.562-1.58430.20431580.18722811X-RAY DIFFRACTION98
1.5843-1.60790.21861460.18942854X-RAY DIFFRACTION100
1.6079-1.63310.2251520.18592861X-RAY DIFFRACTION98
1.6331-1.65980.24081580.18792814X-RAY DIFFRACTION100
1.6598-1.68840.23521360.18462901X-RAY DIFFRACTION99
1.6884-1.71920.21171470.17772866X-RAY DIFFRACTION100
1.7192-1.75220.21481680.17932859X-RAY DIFFRACTION99
1.7522-1.7880.22371610.1832813X-RAY DIFFRACTION100
1.788-1.82690.23911730.18462856X-RAY DIFFRACTION99
1.8269-1.86940.22211590.17492863X-RAY DIFFRACTION100
1.8694-1.91610.20061800.1762851X-RAY DIFFRACTION99
1.9161-1.96790.22171480.17922900X-RAY DIFFRACTION99
1.9679-2.02580.21650.182824X-RAY DIFFRACTION99
2.0258-2.09120.20181610.17082858X-RAY DIFFRACTION99
2.0912-2.1660.22051430.16992891X-RAY DIFFRACTION99
2.166-2.25270.19681460.16962878X-RAY DIFFRACTION99
2.2527-2.35520.1941570.17372864X-RAY DIFFRACTION99
2.3552-2.47940.21931400.17542883X-RAY DIFFRACTION99
2.4794-2.63470.21591420.18532884X-RAY DIFFRACTION99
2.6347-2.83810.25111580.18132856X-RAY DIFFRACTION99
2.8381-3.12370.17771660.18352899X-RAY DIFFRACTION99
3.1237-3.57550.18841500.16712879X-RAY DIFFRACTION99
3.5755-4.50420.15651530.15212921X-RAY DIFFRACTION99
4.5042-47.29510.21271660.17832994X-RAY DIFFRACTION99

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