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

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Basic information

Entry
Database: PDB / ID: 5cbs
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the antagonist (R)-2-amino-3-(3'-hydroxybiphenyl-3-yl)propanoic acid at 1.8A resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor ligand-binding domain / GluA2-S1S2J / antagonist / signaling protein
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / dendritic shaft / SNARE binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / 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
Chem-E42 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsFrydenvang, K. / Kastrup, J.S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Studies on Aryl-Substituted Phenylalanines: Synthesis, Activity, and Different Binding Modes at AMPA Receptors.
Authors: Szymanska, E. / Frydenvang, K. / Pickering, D.S. / Krintel, C. / Nielsen, B. / Kooshki, A. / Zachariassen, L.G. / Olsen, L. / Kastrup, J.S. / Johansen, T.N.
History
DepositionJul 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)120,37737
Polymers117,1154
Non-polymers3,26333
Water25,3291406
1
A: Glutamate receptor 2,Glutamate receptor 2
C: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,11217
Polymers58,5572
Non-polymers1,55515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor 2,Glutamate receptor 2
D: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,26520
Polymers58,5572
Non-polymers1,70818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.468, 92.202, 197.476
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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: 29278.732 Da / Num. of mol.: 4 / Fragment: UNP residues 413-527,UNP residues 653-797
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

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Non-polymers , 6 types, 1439 molecules

#2: Chemical
ChemComp-E42 / (R)-2-amino-3-(3'-hydroxybiphenyl-3-yl)propanoic acid


Mass: 257.284 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H15NO3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1406 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG2000, lithium sulfate and phosphate-citrate buffer pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.801→197.476 Å / Num. all: 96675 / Num. obs: 96675 / % possible obs: 92.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.32 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.084 / Rsym value: 0.074 / Net I/av σ(I): 5.654 / Net I/σ(I): 14.8 / Num. measured all: 425624
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.92.20.265230238135180.1980.2652.790.6
1.9-2.014.40.2282.750601113720.1180.2285.979.5
2.01-2.154.90.1424.265555134840.0710.1429.2100
2.15-2.324.60.2431.247157103360.1430.2439.582.4
2.32-2.554.90.0837.356889116030.0410.08314.5100
2.55-2.854.90.0649.951606105060.0320.06418.8100
2.85-3.294.90.04912.54589693660.0240.04924.8100
3.29-4.024.70.04313.33162566770.0220.04328.784.3
4.02-5.694.80.03713.42997362470.0180.03733100
5.69-29.5474.50.02916.91608435660.0150.02929.998.9

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Processing

Software
NameVersionClassification
SCALA3.3.9data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N0T

1n0t


Resolution: 1.801→29.345 Å / FOM work R set: 0.8674 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 4826 5.02 %Random selection
Rwork0.1669 91247 --
obs0.1695 96073 91.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.71 Å2 / Biso mean: 13.59 Å2 / Biso min: 1.63 Å2
Refinement stepCycle: final / Resolution: 1.801→29.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8123 0 207 1406 9736
Biso mean--23.02 20.16 -
Num. residues----1042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068546
X-RAY DIFFRACTIONf_angle_d1.00511484
X-RAY DIFFRACTIONf_chiral_restr0.0721254
X-RAY DIFFRACTIONf_plane_restr0.0041426
X-RAY DIFFRACTIONf_dihedral_angle_d14.1513236
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8006-1.8210.30361540.22342608276281
1.821-1.84250.2291780.19322836301488
1.8425-1.86490.26861650.19272968313390
1.8649-1.88850.24221540.18763101325595
1.8885-1.91340.27211370.20142423256078
1.9134-1.93960.2632680.19691283135171
1.9396-1.96730.25831690.192132853454100
1.9673-1.99660.22471600.17332583418100
1.9966-2.02780.21961780.158732713449100
2.0278-2.06110.23181830.159432883471100
2.0611-2.09660.25311820.168632793461100
2.0966-2.13470.21721870.166432863473100
2.1347-2.17580.22571340.166532953429100
2.1758-2.22020.21061570.168633113468100
2.2202-2.26840.4444700.36151487155766
2.2684-2.32120.21771580.15772555271389
2.3212-2.37920.20841810.170132973478100
2.3792-2.44350.24321630.173532923455100
2.4435-2.51540.22241670.163833163483100
2.5154-2.59650.24681990.160533053504100
2.5965-2.68920.2111820.161833003482100
2.6892-2.79680.23591720.168333413513100
2.7968-2.9240.23931650.171933173482100
2.924-3.0780.23171640.170933583522100
3.078-3.27060.2111840.164332933477100
3.2706-3.52280.18961770.156633473524100
3.5228-3.87660.18411240.1462611273578
3.8766-4.43590.16451540.13432967312199
4.4359-5.58240.17111720.139634433615100
5.5824-29.34910.19831880.1743526371499

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