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- PDB-3h06: Crystal structure of the binding domain of the AMPA subunit GluR2... -

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Basic information

Entry
Database: PDB / ID: 3h06
TitleCrystal structure of the binding domain of the AMPA subunit GluR2 bound to the willardiine antagonist, UBP282
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / glutamate receptor / glur2 / AMPA receptor / neurotransmitter receptor / S1S2 / willardiine
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 / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic transmission, glutamatergic / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / 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 / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / 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-VBP / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAhmed, A.H. / Oswald, R.E.
CitationJournal: Biochemistry / Year: 2009
Title: Mechanisms of antagonism of the GluR2 AMPA receptor: structure and dynamics of the complex of two willardiine antagonists with the glutamate binding domain.
Authors: Ahmed, A.H. / Thompson, M.D. / Fenwick, M.K. / Romero, B. / Loh, A.P. / Jane, D.E. / Sondermann, H. / Oswald, R.E.
History
DepositionApr 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Glutamate receptor 2
B: Glutamate receptor 2
E: Glutamate receptor 2
H: Glutamate receptor 2
J: Glutamate receptor 2
L: Glutamate receptor 2
N: Glutamate receptor 2
P: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,34916
Polymers230,6838
Non-polymers2,6668
Water5,260292
1
G: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1692
Polymers28,8351
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1692
Polymers28,8351
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1692
Polymers28,8351
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
H: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1692
Polymers28,8351
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
J: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1692
Polymers28,8351
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
L: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1692
Polymers28,8351
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
N: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1692
Polymers28,8351
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
P: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1692
Polymers28,8351
Non-polymers3331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
B: Glutamate receptor 2
hetero molecules

N: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3374
Polymers57,6712
Non-polymers6672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
10
E: Glutamate receptor 2
P: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3374
Polymers57,6712
Non-polymers6672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
G: Glutamate receptor 2
J: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3374
Polymers57,6712
Non-polymers6672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
H: Glutamate receptor 2
L: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3374
Polymers57,6712
Non-polymers6672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.013, 90.916, 92.510
Angle α, β, γ (deg.)85.61, 85.52, 72.40
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glutamate receptor 2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / AMPA-selective glutamate receptor 2


Mass: 28835.320 Da / Num. of mol.: 8 / Fragment: UNP residues 414-527, 652-794
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 (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491
#2: Chemical
ChemComp-VBP / 4-({3-[(2R)-2-amino-2-carboxyethyl]-2,6-dioxo-3,6-dihydropyrimidin-1(2H)-yl}methyl)benzoic acid / (S)-1-(2-amino-2-carboxyethyl)-3-(4-carboxybenzyl)pyrimidine-2,4-dione


Mass: 333.296 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H15N3O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15-17% PEG8K, 0.2 M Na acetate, 0.2 M Na cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2007
RadiationMonochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 64109 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 1.84
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.84 / Rsym value: 0.372 / % possible all: 79

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.71 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2948 6536 -RANDOM
Rwork0.2295 ---
obs-64109 93.5 %-
Displacement parametersBiso mean: 1.639 Å2
Baniso -1Baniso -2Baniso -3
1-6.662 Å25.107 Å2-5.199 Å2
2--1.232 Å2-4.089 Å2
3----7.894 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.38 Å
Luzzati sigma a0.61 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16080 0 192 292 16564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.377 969 -
Rwork0.324 --
obs-8860 84.9 %

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