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- PDB-4yu0: Crystal structure of a tetramer of GluA2 TR mutant ligand binding... -

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Basic information

Entry
Database: PDB / ID: 4yu0
TitleCrystal structure of a tetramer of GluA2 TR mutant ligand binding domains bound with glutamate at 1.26 Angstrom resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsTRANSPORT PROTEIN / tetramer / ligand-gated ion channel
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 / cellular response to glycine / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / ionotropic glutamate receptor binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / somatodendritic compartment / glutamate-gated calcium ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / 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 / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase 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
GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsChebli, M. / Salazar, H. / Baranovic, J. / Carbone, A.L. / Ghisi, V. / Faelber, K. / Lau, A.Y. / Daumke, O. / Plested, A.J.R.
CitationJournal: To Be Published
Title: Crystal structure of the tetrameric GluA2 ligand-binding domain in complex with glutamate at 1.26 Angstroms resolution
Authors: Chebli, M. / Salazar, H. / Baranovic, J. / Carbone, A.L. / Ghisi, V. / Faelber, K. / Lau, A.Y. / Daumke, O. / Plested, A.J.R.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 2.0Mar 31, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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 2.2Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,66414
Polymers58,3752
Non-polymers1,28912
Water14,808822
1
A: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8327
Polymers29,1881
Non-polymers6446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8327
Polymers29,1881
Non-polymers6446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.140, 47.420, 116.940
Angle α, β, γ (deg.)90.00, 93.59, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-697-

HOH

21B-647-

HOH

31B-655-

HOH

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Components

#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: 29187.697 Da / Num. of mol.: 2 / Mutation: E713T, Y768R,E713T, Y768R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.96 % / Description: cube-like crystals
Crystal growTemperature: 277.14 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% w/v PEG3350 and 200 mM (NH4)2HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 10, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.26→50 Å / Num. all: 138023 / Num. obs: 138023 / % possible obs: 99.1 % / Redundancy: 3.9 % / Rsym value: 0.05 / Net I/σ(I): 14.3
Reflection shellResolution: 1.26→1.29 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.428 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
MOSFLMdata reduction
PHASERphasing
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 1.26→47.047 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 13.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1574 7022 5.09 %random selection
Rwork0.1292 ---
obs0.1306 138019 99.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.26→47.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 78 822 4938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144384
X-RAY DIFFRACTIONf_angle_d1.5495929
X-RAY DIFFRACTIONf_dihedral_angle_d12.8031723
X-RAY DIFFRACTIONf_chiral_restr0.1657
X-RAY DIFFRACTIONf_plane_restr0.008738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.27430.23452130.20873877X-RAY DIFFRACTION89
1.2743-1.28930.24251920.19864107X-RAY DIFFRACTION94
1.2893-1.3050.20582320.17944317X-RAY DIFFRACTION98
1.305-1.32160.19562700.16174332X-RAY DIFFRACTION99
1.3216-1.33890.19332430.15154321X-RAY DIFFRACTION100
1.3389-1.35730.17982150.13874447X-RAY DIFFRACTION100
1.3573-1.37670.1862240.13734297X-RAY DIFFRACTION100
1.3767-1.39720.16222240.14074423X-RAY DIFFRACTION100
1.3972-1.41910.17852500.13394352X-RAY DIFFRACTION100
1.4191-1.44230.17662180.12884376X-RAY DIFFRACTION100
1.4423-1.46720.17272420.12344376X-RAY DIFFRACTION100
1.4672-1.49390.15782200.11634376X-RAY DIFFRACTION100
1.4939-1.52260.1452170.11244457X-RAY DIFFRACTION100
1.5226-1.55370.14472300.10754354X-RAY DIFFRACTION100
1.5537-1.58750.13842280.10934378X-RAY DIFFRACTION100
1.5875-1.62440.14542320.10854408X-RAY DIFFRACTION100
1.6244-1.6650.1572420.1044360X-RAY DIFFRACTION100
1.665-1.71010.12612150.10614421X-RAY DIFFRACTION100
1.7101-1.76040.16042500.11124420X-RAY DIFFRACTION100
1.7604-1.81720.15852590.11344341X-RAY DIFFRACTION100
1.8172-1.88220.14692430.11424373X-RAY DIFFRACTION100
1.8822-1.95750.15262660.11654369X-RAY DIFFRACTION99
1.9575-2.04660.12682310.11684388X-RAY DIFFRACTION100
2.0466-2.15450.15482520.12194394X-RAY DIFFRACTION100
2.1545-2.28950.14162240.12174363X-RAY DIFFRACTION99
2.2895-2.46630.15552250.13014453X-RAY DIFFRACTION100
2.4663-2.71440.16312350.14014398X-RAY DIFFRACTION100
2.7144-3.10710.17032400.14674466X-RAY DIFFRACTION100
3.1071-3.91440.14422400.12984498X-RAY DIFFRACTION100
3.9144-47.08020.15742500.13594555X-RAY DIFFRACTION100

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