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- PDB-2cmo: The structure of a mixed glur2 ligand-binding core dimer in compl... -

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Basic information

Entry
Database: PDB / ID: 2cmo
TitleThe structure of a mixed glur2 ligand-binding core dimer in complex with (s)-glutamate and the antagonist (s)-ns1209
ComponentsGLUTAMATE RECEPTOR 2
KeywordsION CHANNEL / MEMBRANE / RECEPTOR / PALMITATE / TRANSPORT / POSTSYNAPTIC MEMBRANE / GLYCOPROTEIN / IONIC CHANNEL / ION TRANSPORT / TRANSMEMBRANE / ALTERNATIVE SPLICING / RNA EDITING / LIPOPROTEIN
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 / receptor internalization / terminal bouton / 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 / Chem-M1L / Glutamate receptor 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKasper, C. / Pickering, D.S. / Mirza, O. / Olsen, L. / Kristensen, A.S. / Greenwood, J.R. / Liljefors, T. / Schousboe, A. / Watjen, F. / Gajhede, M. ...Kasper, C. / Pickering, D.S. / Mirza, O. / Olsen, L. / Kristensen, A.S. / Greenwood, J.R. / Liljefors, T. / Schousboe, A. / Watjen, F. / Gajhede, M. / Sigurskjold, B.W. / Kastrup, J.S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Structure of a Mixed Glur2 Ligand-Binding Core Dimer in Complex with (S)-Glutamate and the Antagonist (S)-Ns1209.
Authors: Kasper, C. / Pickering, D.S. / Mirza, O. / Olsen, L. / Kristensen, A.S. / Greenwood, J.R. / Liljefors, T. / Schousboe, A. / Watjen, F. / Gajhede, M. / Sigurskjold, B.W. / Kastrup, J.S.
History
DepositionMay 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 28, 2021Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / reflns / struct_site
Item: _chem_comp.pdbx_synonyms / _reflns.pdbx_redundancy ..._chem_comp.pdbx_synonyms / _reflns.pdbx_redundancy / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 13, 2023Group: 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
B: GLUTAMATE RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4938
Polymers58,4432
Non-polymers1,0506
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.554, 92.953, 96.454
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUTAMATE RECEPTOR 2 / GLUR2 LIGAND-BINDING CORE / S1S2J / GLUR-2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC / ...GLUR2 LIGAND-BINDING CORE / S1S2J / GLUR-2 / GLUR-B / GLUR-K2 / GLUTAMATE RECEPTOR IONOTROPIC / AMPA 2 / AMPA-SELECTIVE GLUTAMATE RECEPTOR 2


Mass: 29221.682 Da / Num. of mol.: 2 / Fragment: RESIDUES 413-527,653-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET30B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19491
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-M1L / 2-({[(3E)-5-{4-[(DIMETHYLAMINO)(DIHYDROXY)-LAMBDA~4~-SULFANYL]PHENYL}-8-METHYL-2-OXO-6,7,8,9-TETRAHYDRO-1H-PYRROLO[3,2-H]ISOQUINOLIN-3(2H)-YLIDENE]AMINO}OXY)-4-HYDROXYBUTANOIC ACID / SPD 502 / NS 1209


Mass: 518.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30N4O7S
#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.: 230 / Source method: isolated from a natural source / Formula: H2O
Compound detailsL-GLUTAMATE ACTS AS AN EXCITATORY NEUROTRANSMITTER AT MANY SYNAPSES IN THE CENTRAL NERVOUS SYSTEM
Sequence detailsNATIVE GLUR2 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING ...NATIVE GLUR2 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING CORE OF GLUR2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 115-116). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (413-527, 653-796). THE TWO FIRST RESIDUES OF THE SEQUENCE (GLY, ALA) ARE CLONING ARTIFACTS AND WERE NOT LOCATED IN THE ELECTRON DENSITY MAP.

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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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growpH: 6.5 / Details: pH 6.50

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 0.976
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 26, 2002
RadiationMonochromator: NOT SPECIFIED. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.65→24.06 Å / Num. obs: 15865 / % possible obs: 88.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6
Reflection shellResolution: 2.65→2.74 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 87.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1FTL AND 1FTJ

1ftl

1ftj


Resolution: 2.65→24.06 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 775 4.9 %RANDOM
Rwork0.215 ---
obs0.215 15865 88.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.5 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2---1.28 Å20 Å2
3----0.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å-
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å-
Refinement stepCycle: LAST / Resolution: 2.65→24.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 66 230 4314
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.641.5
X-RAY DIFFRACTIONc_mcangle_it1.142
X-RAY DIFFRACTIONc_scbond_it0.892
X-RAY DIFFRACTIONc_scangle_it1.442.5
LS refinement shellResolution: 2.65→2.76 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 110 4.4 %
Rwork0.288 2366 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5SPD_PAR.TXTSPD_TOP.TXT

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