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

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Basic information

Entry
Database: PDB / ID: 5fho
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with (S)-2-Amino-3-(5-(2-(3-chlorobenzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at 2.3 A resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / Ionotropic glutamate receptor GluA2 / ligand-binding domain / 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-5XN / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFrydenvang, K. / Kastrup, J.S.
Citation
Journal: J.Med.Chem. / Year: 2016
Title: Tweaking Subtype Selectivity and Agonist Efficacy at (S)-2-Amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)propionic acid (AMPA) Receptors in a Small Series of BnTetAMPA Analogues.
Authors: Wang, S.Y. / Larsen, Y. / Navarrete, C.V. / Jensen, A.A. / Nielsen, B. / Al-Musaed, A. / Frydenvang, K. / Kastrup, J.S. / Pickering, D.S. / Clausen, R.P.
#1: Journal: J. Med. Chem. / Year: 2007
Title: A tetrazolyl-substituted subtype-selective AMPA receptor agonist.
Authors: Vogensen, S.B. / Frydenvang, K. / Greenwood, J.R. / Postorino, G. / Nielsen, B. / Pickering, D.S. / Ebert, B. / Bolcho, U. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. / Johansen, T.N. / ...Authors: Vogensen, S.B. / Frydenvang, K. / Greenwood, J.R. / Postorino, G. / Nielsen, B. / Pickering, D.S. / Ebert, B. / Bolcho, U. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. / Johansen, T.N. / Clausen, R.P. / Krogsgaard-Larsen, P.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 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 1.4Nov 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 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)121,66650
Polymers117,1154
Non-polymers4,55146
Water7,440413
1
A: Glutamate receptor 2,Glutamate receptor 2
D: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,72325
Polymers58,5572
Non-polymers2,16623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-79 kcal/mol
Surface area22750 Å2
MethodPISA
2
B: Glutamate receptor 2,Glutamate receptor 2
C: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,94225
Polymers58,5572
Non-polymers2,38523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-88 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.983, 109.982, 144.208
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 / Ionotropic glutamate receptor A2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2 Ionotropic glutamate receptor A2 /


Mass: 29278.732 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions genetically removed and replaced with Gly-Thr linker (residues 118-119). Protein consists of ...Details: Protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions genetically removed and replaced with Gly-Thr linker (residues 118-119). Protein consists of UNP residues 413-527 and 653-797, numbering with signal peptide of 21 residues. The first two residues (Gly, Ala) are cloning remnants.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

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Non-polymers , 7 types, 459 molecules

#2: Chemical
ChemComp-5XN / (1S)-1-carboxy-2-(5-{2-[(3-chlorophenyl)methyl]-2H-tetrazol-5-yl}-3-oxo-2,3-dihydro-1,2-oxazol-4-yl)ethan-1-aminium


Mass: 365.752 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H14ClN6O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG4000 ammonium sulfate acetate buffer pH 5.5 / PH range: 5.5

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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: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.07 Å / Num. all: 50972 / Num. obs: 50972 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 28.03 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Rsym value: 0.067 / Net I/av σ(I): 9 / Net I/σ(I): 14.6 / Num. measured all: 208313
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
2.3-2.424.10.33123000473330.1840.3315100
2.42-2.574.10.262.62864469340.1440.266.2100
2.57-2.754.10.1733.92700865470.0960.1738.4100
2.75-2.974.10.1255.52523361190.070.12510.7100
2.97-3.254.10.0828.22328456510.0460.08214.9100
3.25-3.644.10.05511.52099751120.0310.05520.8100
3.64-4.24.10.03915.51865145540.0220.03926.4100
4.2-5.144.10.03117.21575138820.0170.03130.4100
5.14-7.2740.03314.51218130600.0190.03323.5100
7.27-45.9563.70.01920.9656017800.0110.01925.499.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P2A (molB)

2p2a


Resolution: 2.3→44.046 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 4917 5.08 %
Rwork0.1726 91903 -
obs0.1747 50882 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.98 Å2 / Biso mean: 36.1995 Å2 / Biso min: 13.77 Å2
Refinement stepCycle: final / Resolution: 2.3→44.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7995 0 472 415 8882
Biso mean--45.89 33 -
Num. residues----1024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028391
X-RAY DIFFRACTIONf_angle_d0.5411258
X-RAY DIFFRACTIONf_chiral_restr0.0421223
X-RAY DIFFRACTIONf_plane_restr0.0031383
X-RAY DIFFRACTIONf_dihedral_angle_d8.765001
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 (%)
2.3-2.32620.26281970.203830543251100
2.3262-2.35350.26491320.218130833215100
2.3535-2.38220.27261740.203530493223100
2.3822-2.41240.241880.192130333221100
2.4124-2.44410.26751560.194730683224100
2.4441-2.47760.24671920.196130503242100
2.4776-2.5130.25491360.193630823218100
2.513-2.55050.20361640.198930583222100
2.5505-2.59030.28971960.191830403236100
2.5903-2.63280.24531460.187931043250100
2.6328-2.67820.27071710.190730613232100
2.6782-2.72690.23681540.183630733227100
2.7269-2.77930.26681590.180230453204100
2.7793-2.83610.24341740.178430563230100
2.8361-2.89770.20311710.162930403211100
2.8977-2.96510.25191570.172231013258100
2.9651-3.03920.22141740.178830583232100
3.0392-3.12140.20131520.180630803232100
3.1214-3.21320.23021660.176430723238100
3.2132-3.31690.20922060.17929953201100
3.3169-3.43540.20411740.16930693243100
3.4354-3.57290.1861670.16130523219100
3.5729-3.73540.19941530.16430953248100
3.7354-3.93220.18611560.15430703226100
3.9322-4.17840.17171690.142230453214100
4.1784-4.50080.16481530.135730823235100
4.5008-4.95310.1571400.137430713211100
4.9531-5.66860.21711500.169930763226100
5.6686-7.13690.28681320.211631003232100
7.1369-44.05420.22621580.19333041319999

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