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- PDB-5nih: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in c... -

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Basic information

Entry
Database: PDB / ID: 5nih
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist LM-12b at 1.3 A resolution.
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / AMPA RECEPTOR / LIGAND-BINDING DOMAIN / GLUA2 / GLUR2 / AGONIST
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel 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 / positive regulation of synaptic transmission / glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel 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 binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / postsynaptic density membrane / modulation of chemical synaptic transmission / establishment of protein localization / Schaffer collateral - CA1 synapse / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / 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 / 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
Chem-8VE / ACETATE ION / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLaulumaa, S. / Frydenvang, K.A. / Kastrup, J.S.
CitationJournal: ACS Chem Neurosci / Year: 2017
Title: Structure and Affinity of Two Bicyclic Glutamate Analogues at AMPA and Kainate Receptors.
Authors: Mllerud, S. / Pinto, A. / Marconi, L. / Frydenvang, K. / Thorsen, T.S. / Laulumaa, S. / Venskutonyte, R. / Winther, S. / Moral, A.M.C. / Tamborini, L. / Conti, P. / Pickering, D.S. / Kastrup, J.S.
History
DepositionMar 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Jan 17, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,96216
Polymers58,5572
Non-polymers1,40514
Water14,034779
1
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,15110
Polymers29,2791
Non-polymers8729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8126
Polymers29,2791
Non-polymers5335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.577, 87.954, 96.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein 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: 29278.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMIAN OF GLUA2. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (118-119). SEQUENCE MATCHES DISCONTINUOUSLY WITH THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMIAN OF GLUA2. TRANSMEMBRANE REGIONS WERE REPLACED WITH A GLY-THR LINKER (118-119). SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (413-527, 653-797). RESIDUES 1-2 ARE CLONING REMNANTS.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

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Non-polymers , 6 types, 793 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Chemical ChemComp-8VE / (3~{a}~{R},4~{S},6~{a}~{R})-1-methyl-4,5,6,6~{a}-tetrahydro-3~{a}~{H}-pyrrolo[3,4-c]pyrazole-3,4-dicarboxylic acid


Mass: 213.191 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N3O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 24.4% PEG4000, 0.3 M ammonium sulfate, 0.1 M phosphate-citrate buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.3→96.535 Å / Num. obs: 131334 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 10.35 Å2 / Rsym value: 0.063 / Net I/σ(I): 14.1
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.465 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.22data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M5B

1m5b


Resolution: 1.3→48.27 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 14.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.158 6452 4.92 %
Rwork0.127 --
obs0.128 131162 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.06 Å2
Refinement stepCycle: LAST / Resolution: 1.3→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 85 779 4931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074571
X-RAY DIFFRACTIONf_angle_d1.0266228
X-RAY DIFFRACTIONf_dihedral_angle_d19.6211805
X-RAY DIFFRACTIONf_chiral_restr0.079685
X-RAY DIFFRACTIONf_plane_restr0.006786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.20311800.16724174X-RAY DIFFRACTION100
1.3148-1.33020.21242230.15854099X-RAY DIFFRACTION100
1.3302-1.34650.18722110.14974099X-RAY DIFFRACTION100
1.3465-1.36350.1772240.14424130X-RAY DIFFRACTION100
1.3635-1.38150.18231980.14244107X-RAY DIFFRACTION100
1.3815-1.40040.1822200.14234119X-RAY DIFFRACTION100
1.4004-1.42040.18492070.13714171X-RAY DIFFRACTION100
1.4204-1.44160.17871960.13584079X-RAY DIFFRACTION100
1.4416-1.46410.19442410.12984089X-RAY DIFFRACTION100
1.4641-1.48810.16961990.12384147X-RAY DIFFRACTION100
1.4881-1.51380.14512040.11534133X-RAY DIFFRACTION100
1.5138-1.54130.16372050.11314137X-RAY DIFFRACTION100
1.5413-1.5710.1472230.11454131X-RAY DIFFRACTION100
1.571-1.6030.15712180.11074107X-RAY DIFFRACTION100
1.603-1.63790.14141930.10934163X-RAY DIFFRACTION100
1.6379-1.6760.15912410.10684099X-RAY DIFFRACTION100
1.676-1.71790.14032050.10534165X-RAY DIFFRACTION100
1.7179-1.76440.1592060.114139X-RAY DIFFRACTION100
1.7644-1.81630.1272210.10844141X-RAY DIFFRACTION100
1.8163-1.87490.13012390.10794132X-RAY DIFFRACTION100
1.8749-1.94190.15342270.10774127X-RAY DIFFRACTION100
1.9419-2.01970.14261970.11264210X-RAY DIFFRACTION100
2.0197-2.11160.14382230.10964147X-RAY DIFFRACTION100
2.1116-2.22290.13872050.11034182X-RAY DIFFRACTION100
2.2229-2.36220.14672260.11164185X-RAY DIFFRACTION100
2.3622-2.54460.15812200.12064194X-RAY DIFFRACTION100
2.5446-2.80060.14382300.12624188X-RAY DIFFRACTION100
2.8006-3.20580.17062180.13594239X-RAY DIFFRACTION100
3.2058-4.03860.15322170.1284285X-RAY DIFFRACTION100
4.0386-48.30080.18352350.17444392X-RAY DIFFRACTION99

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