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- PDB-6yk5: Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2... -

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Basic information

Entry
Database: PDB / ID: 6yk5
TitleStructure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound (S)-1-(2'-Amino-2'-carboxyethyl)-5,7-dihydrofuro[3,4-d]- pyrimidine-2,4(1H,3H)-dione at resolution 1.15A
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / GLUA2O LIGAND-BINDING DOMAIN / BICYCLIC PYRIMIDINEDIONE ANALOGUE
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 I
Similarity search - Domain/homology
: / Chem-PVK / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsFrydenvang, K. / Kastrup, J.S.
CitationJournal: Acs Chem Neurosci / Year: 2020
Title: Ionotropic Glutamate Receptor GluA2 in Complex with Bicyclic Pyrimidinedione-Based Compounds: When Small Compound Modifications Have Distinct Effects on Binding Interactions.
Authors: Frydenvang, K. / Pickering, D.S. / Kshirsagar, G.U. / Chemi, G. / Gemma, S. / Sprogoe, D. / Kærn, A.M. / Brogi, S. / Campiani, G. / Butini, S. / Kastrup, J.S.
History
DepositionApr 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 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
A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,50714
Polymers29,2791
Non-polymers1,22813
Water8,035446
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,01428
Polymers58,5572
Non-polymers2,45726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5540 Å2
ΔGint-150 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.075, 96.331, 48.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-487-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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.: 1
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2O. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUE 118-119). THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2O. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUE 118-119). THE SEQUENCE MATCHES DISCONTINOUSLY WITH THE REFERENCE DATABASE (UNP RESIDUES 413-527 AND 653-797, NUMBERING WITH SIGNAL PEPTIDE OF 21 AMINO ACIDS). THE TWO FIRST RESIDUES (GLY, ALA) ARE CLONING REMNANTS.
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 (DE3) / References: UniProt: P19491

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Non-polymers , 6 types, 459 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Chemical ChemComp-PVK / (S)-1-(2'-Amino-2'-carboxyethyl)-5,7-dihydrofuro[3,4-d]-pyrimidine-2,4(1H,3H)-dione / (2~{S})-2-azanyl-3-[2,4-bis(oxidanylidene)furo[3,4-d]pyrimidin-1-yl]propanoic acid


Mass: 241.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11N3O5 / Feature type: SUBJECT OF INVESTIGATION
#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.: 446 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG4000, lithium sulfate, acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→28.212 Å / Num. all: 97655 / Num. obs: 97655 / % possible obs: 98.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 7.97 Å2 / Rpim(I) all: 0.032 / Rrim(I) all: 0.069 / Rsym value: 0.061 / Net I/av σ(I): 7.6 / Net I/σ(I): 14.2 / Num. measured all: 450981
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.15-1.213.40.385244337129820.2310.4520.3853.290.7
1.21-1.294.70.312.563004135200.160.3490.314.9100
1.29-1.374.70.2173.560468127310.1110.2450.2176.6100
1.37-1.484.80.1485.257141118940.0750.1660.1489.1100
1.48-1.634.90.0977.853300109820.0490.1090.09713.1100
1.63-1.824.90.06910.44857599610.0350.0770.06917.6100
1.82-2.14.90.05112.54327688170.0260.0580.05124.2100
2.1-2.574.90.04314.13695175270.0220.0490.04330.1100
2.57-3.644.90.03714.72868558820.0190.0420.03734.3100
3.64-26.7784.50.03515.71524433590.0190.040.03535.799

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Processing

Software
NameVersionClassification
SCALA3.3.9data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SYH

1syh


Resolution: 1.15→26.778 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 9.7
RfactorNum. reflection% reflection
Rfree0.1301 4873 4.99 %
Rwork0.1098 --
obs0.1108 97582 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 55.22 Å2 / Biso mean: 12.6496 Å2 / Biso min: 4.09 Å2
Refinement stepCycle: final / Resolution: 1.15→26.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 73 457 2543
Biso mean--17.43 25.7 -
Num. residues----263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.15-1.16310.26471080.2211215069
1.1631-1.17680.19331390.1958279390
1.1768-1.19110.19211570.16723098100
1.1911-1.20620.15791420.15043123100
1.2062-1.22210.18351730.13993058100
1.2221-1.23880.17521520.12733129100
1.2388-1.25650.1611660.12073116100
1.2565-1.27520.13231470.11573096100
1.2752-1.29520.14751500.11343113100
1.2952-1.31640.12971520.10343135100
1.3164-1.33910.14321770.09953075100
1.3391-1.36350.13971600.09693116100
1.3635-1.38970.11971820.09183091100
1.3897-1.4180.10651720.08693107100
1.418-1.44890.11941710.08913077100
1.4489-1.48260.11741800.08773130100
1.4826-1.51960.12061860.08113103100
1.5196-1.56070.11141480.07773121100
1.5607-1.60670.11011840.07463083100
1.6067-1.65850.10471490.07623163100
1.6585-1.71780.11161640.0793111100
1.7178-1.78650.10591780.08173143100
1.7865-1.86780.10011870.08543122100
1.8678-1.96630.10931680.09023147100
1.9663-2.08940.11411260.09013174100
2.0894-2.25070.11421720.09523168100
2.2507-2.4770.11071740.1073170100
2.477-2.83510.13051650.11873223100
2.8351-3.57060.13461710.12263214100
3.5706-26.7780.15881730.1498336099

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