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- PDB-6fqg: GluA2(flop) G724C ligand binding core dimer bound to L-Glutamate ... -

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Basic information

Entry
Database: PDB / ID: 6fqg
TitleGluA2(flop) G724C ligand binding core dimer bound to L-Glutamate (Form A) at 2.34 Angstrom resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPAR receptor / Ligand binding domain / Competitive antagonist / Cross-linked dimer
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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.34139094861 Å
AuthorsCoombs, I.D. / Soto, D. / Gold, M.G. / Farrant, M.F. / Cull-Candy, S.G.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/J002976/1 United Kingdom
Medical Research Council (United Kingdom)MR/J012998/1 United Kingdom
Wellcome Trust086185/Z/08/Z United Kingdom
CitationJournal: To Be Published
Title: X-ray structure of GluA2 flop G724C ligand binding core dimer bound to glutamate at 2.32 Angstroms resolution
Authors: Coombs, I.D. / Soto, D. / Gold, M.G. / Farrant, M.F. / Cull-Candy, S.G.
History
DepositionFeb 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 2.0Mar 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_mutation / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9444
Polymers58,6502
Non-polymers2942
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Ion channel properties were changed by cross-linking.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-6 kcal/mol
Surface area24640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.465, 87.655, 68.280
Angle α, β, γ (deg.)90.000, 110.223, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: CYS / End label comp-ID: CYS / Auth seq-ID: 4 - 261 / Label seq-ID: 4 - 261

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A'AA
2(chain 'B' and resid 4 through 261)BB

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Components

#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: 29324.826 Da / Num. of mol.: 2 / Mutation: S729C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22B / Production host: Escherichia coli K-12 (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.2M Ammonium chloride, 20% PEG 3350, 10uM ZK200775

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.98→92.4 Å / Num. obs: 45174 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.987 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.064 / Rrim(I) all: 0.09 / Net I/σ(I): 12.9 / Num. measured all: 88738
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.98-2.0321.26731420.231.2671.79299.8
9.07-92.41.80.0114940.9990.0110.015100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
Aimless0.5.27data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGC

3kgc


Resolution: 2.34139094861→51.7259332996 Å / SU ML: 0.299678746971 / Cross valid method: THROUGHOUT / σ(F): 1.35058517464 / Phase error: 25.6970227284
RfactorNum. reflection% reflection
Rfree0.23094510633 2157 4.92589463107 %
Rwork0.178606277062 --
obs0.181217507374 43789 94.6584522265 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.9071580163 Å2
Refinement stepCycle: LAST / Resolution: 2.34139094861→51.7259332996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 20 104 4166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134177079364135
X-RAY DIFFRACTIONf_angle_d1.26155690735560
X-RAY DIFFRACTIONf_chiral_restr0.0628884776573616
X-RAY DIFFRACTIONf_plane_restr0.00772228584667694
X-RAY DIFFRACTIONf_dihedral_angle_d14.49968990352514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3414-2.39590.347819474941060.3098183642072568X-RAY DIFFRACTION86.036036036
2.3959-2.45580.3649835014231550.2699080617152773X-RAY DIFFRACTION96.0945191992
2.4558-2.52220.2711489911061420.2618719315362865X-RAY DIFFRACTION95.9476707084
2.5222-2.59640.3052258459181620.2522925483392727X-RAY DIFFRACTION95.3780125454
2.5964-2.68020.3636387708041550.2442123615822772X-RAY DIFFRACTION93.8441808272
2.6802-2.7760.2907975085531110.2420101608942692X-RAY DIFFRACTION90.4485317844
2.776-2.88710.2657027504261610.2144461057492762X-RAY DIFFRACTION96.4686468647
2.8871-3.01850.2119767925861340.2092455437992854X-RAY DIFFRACTION96.138996139
3.0185-3.17760.2545833901031040.2045630897782899X-RAY DIFFRACTION96.7461340206
3.1776-3.37670.2269480743261800.1721460443422819X-RAY DIFFRACTION96.8356474007
3.3767-3.63730.2393511228531440.1645705661152664X-RAY DIFFRACTION92.1864740643
3.6373-4.00320.2237233788161160.1466559575172894X-RAY DIFFRACTION97.537265068
4.0032-4.58220.178669960181320.1266772699362870X-RAY DIFFRACTION96.6205342774
4.5822-5.77190.1703963957161640.1467673258662694X-RAY DIFFRACTION93.4903500164
5.7719-51.73850.221336441451910.1613529997182779X-RAY DIFFRACTION96.2722852512

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