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

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Basic information

Entry
Database: PDB / ID: 6fqi
TitleGluA2(flop) G724C ligand binding core dimer bound to L-Glutamate (Form B) at 2.91 Angstrom resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPAR receptor / Ligand binding domain / glutamate / 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 / Resolution: 2.91001156656 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: Nat Commun / Year: 2019
Title: Homomeric GluA2(R) AMPA receptors can conduct when desensitized.
Authors: Coombs, I.D. / Soto, D. / McGee, T.P. / Gold, M.G. / Farrant, M. / Cull-Candy, S.G.
History
DepositionFeb 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Mar 15, 2023Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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_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 / _pdbx_validate_close_contact.auth_comp_id_2 / _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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-7 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.650, 50.650, 256.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
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
1(chain 'A' and (resid 4 through 21 or (resid 22...AA
2(chain 'B' and (resid 4 through 20 or (resid 21...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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / 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

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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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16 M Calcium acetate, 0.08 M Sodium Cacodylate, 14.4% (w/v) PEG 8000, 20% (v/v) Glycerol, 1 mM glutamate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.91→50.65 Å / Num. obs: 13984 / % possible obs: 99.6 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rpim(I) all: 0.068 / Rrim(I) all: 0.121 / Net I/σ(I): 10.7
Reflection shellResolution: 2.91→3.01 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimlessdata scaling
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 2.91001156656→50.65 Å / SU ML: 0.501308766165 / Cross valid method: FREE R-VALUE / σ(F): 1.35079047219 / Phase error: 29.7490196354
RfactorNum. reflection% reflection
Rfree0.267057246139 662 4.73398169336 %
Rwork0.213532833816 --
obs0.216100836964 13984 99.1843393148 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 80.834449764 Å2
Refinement stepCycle: LAST / Resolution: 2.91001156656→50.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4009 0 20 0 4029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002674604351314102
X-RAY DIFFRACTIONf_angle_d0.7046817849895520
X-RAY DIFFRACTIONf_chiral_restr0.042370911724609
X-RAY DIFFRACTIONf_plane_restr0.00323618220638694
X-RAY DIFFRACTIONf_dihedral_angle_d15.37618565752469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.13470.3518671060511430.3373311460862656X-RAY DIFFRACTION99.0095507605
3.1347-3.45010.3073177366351530.2718505118952630X-RAY DIFFRACTION99.428367274
3.4501-3.94910.3311865453381260.2268194146792670X-RAY DIFFRACTION98.9384288747
3.9491-4.97480.2690817506971050.1745426752662688X-RAY DIFFRACTION99.5012468828
4.9748-50.65760.1952984047181350.1807768404032678X-RAY DIFFRACTION99.0492957746
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.519740586070.636453053062-0.4459802685712.333817850860.0861919268864.02313619546-0.131807478411-0.115298399872-0.07168035576380.1274711396520.0247207961883-0.00684951491034-0.4724828861080.1365487539490.04252428025370.354487635041-0.0048265664986-0.0297620097870.389473364694-0.02542267471550.37224264018820.4686218896-0.97728859699667.2246893668
22.540593421230.8888346893680.03369170552332.569130958020.2048697867983.463489552320.162520336567-0.0981570619539-0.2203707989570.134530914778-0.07688059809820.2512846359850.128996923115-0.598447227032-0.1675628156790.272064493827-0.0221656665774-0.04633066727050.607994262837-0.003105960969010.497594522191.16240984252-17.223063981468.5866200245
31.379167405761.33235464558-1.037645804013.4413161239-0.5790948273111.89322411215-0.178926095420.260846921541-0.00629648881992-0.554082740880.3981975897730.02964726913440.0323127361789-0.306447457631-0.1780560984330.3977023502910.0981197089938-0.1064244292720.608149180936-0.04568815788130.43292482005813.3750172731-9.7451893276357.7242626904
42.695523382731.237230317560.5094750575451.237089198111.161430331644.801512116970.0975259526004-0.437324453458-0.439975405997-0.118942695110.3357326359040.0505823740280.135934109328-0.502942593067-0.2241672307120.515878534016-0.17181564834-0.1094387874410.4975320342530.1799364455820.534986308841-14.5372663818-26.780501330827.0787645161
55.56963340919-0.06246320517531.830105791512.182602473452.441238385674.36195924878-0.591218763493-0.1287330231040.5420122371891.077483456990.360120583098-0.502441997716-1.071276706781.054608794050.1009707089921.07910207579-0.180257098041-0.112767238360.9139884103580.06785939016060.4678034963296.81936521839-10.352072901740.5794599475
63.600079002950.560031946131.019581344264.82547571505-0.8172697051527.4330670693-0.0124520929929-0.09954018826370.2751221640880.4315094172440.141420527069-0.167734572992-1.000694134710.91516734374-0.1211451449560.747556078317-0.10171418345-0.009151533026460.627518676675-0.04896348624770.4780183763170.744437979077-12.419907844732.748365177
70.2892285718350.258317818876-1.001011455043.60674662132-0.3124885790113.56852012308-0.117831101732-1.10085379632-0.04547541574330.4715187427720.4903313154680.555627298839-0.0239687943506-0.95316479723-0.4142220531540.712489795172-0.0448261230520.01749021515880.9485062040080.3041830058050.568116229553-13.2383085055-24.241071885638.2839156212
85.947126224431.38067697442.289629573321.8522648991.962585056482.577631685931.19414397924-1.64523246681-1.32493469043-0.0199001692285-0.2628598232330.02909565062680.201009490328-0.779875129949-0.6472192026451.14018215774-0.0474074207538-0.2159494948920.7152026634210.2058650913130.747108979373-6.38800255155-33.757114145844.1044367548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 173 )
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 262 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 110 )
5X-RAY DIFFRACTION5chain 'B' and (resid 111 through 137 )
6X-RAY DIFFRACTION6chain 'B' and (resid 138 through 201 )
7X-RAY DIFFRACTION7chain 'B' and (resid 202 through 243 )
8X-RAY DIFFRACTION8chain 'B' and (resid 244 through 264 )

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