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- PDB-6fqh: GluA2(flop) S729C ligand binding core dimer bound to NBQX at 1.76... -

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Basic information

Entry
Database: PDB / ID: 6fqh
TitleGluA2(flop) S729C ligand binding core dimer bound to NBQX at 1.76 Angstrom resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPAR receptor / Ligand binding core / Competitive antagonist
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 calcium ion channel activity / 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 / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / modulation of chemical synaptic transmission / establishment of protein localization / 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 / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / 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
Chem-E2Q / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75940018229 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: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 1.2Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5064
Polymers60,8342
Non-polymers6732
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-7 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.107, 108.107, 99.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
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: 16 - 273

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1(chain 'A' and resid 4 through 261)AA
2(chain 'B' and (resid 4 through 20 or (resid 21...BB

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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: 30416.953 Da / Num. of mol.: 2 / Mutation: S729C,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-E2Q / 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide


Mass: 336.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H8N4O6S / Comment: antagonist*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M tri-sodium Citrate, 20% PEG 3000

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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: 1.7594→54.0535 Å / Num. obs: 65151 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 1 / Rpim(I) all: 0.016 / Rrim(I) all: 0.041 / Net I/σ(I): 23.1
Reflection shellResolution: 1.76→1.79 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
Aimless0.5.26data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGC

3kgc


Resolution: 1.75940018229→54.0535 Å / SU ML: 0.258475640504 / Cross valid method: THROUGHOUT / σ(F): 1.33532995095 / Phase error: 26.1722097045
RfactorNum. reflection% reflection
Rfree0.223979280802 3243 5.01515526413 %
Rwork0.189312538281 --
obs0.191023582719 64664 99.2784106611 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.9676519647 Å2
Refinement stepCycle: LAST / Resolution: 1.75940018229→54.0535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4027 0 46 458 4531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01104994048544152
X-RAY DIFFRACTIONf_angle_d1.172386175365599
X-RAY DIFFRACTIONf_chiral_restr0.0633141882317611
X-RAY DIFFRACTIONf_plane_restr0.00755573959985695
X-RAY DIFFRACTIONf_dihedral_angle_d13.15680444872490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7594-1.78570.3921262921881510.4087259997942532X-RAY DIFFRACTION94.6718419195
1.7857-1.81360.35620535851400.3759912348152614X-RAY DIFFRACTION97.8330373002
1.8136-1.84330.4323895306431330.353143078772640X-RAY DIFFRACTION98.1245576787
1.8433-1.87510.4105460378511360.3318822106772630X-RAY DIFFRACTION98.5042735043
1.8751-1.90920.3282958837881520.3051577342922640X-RAY DIFFRACTION99.1125310614
1.9092-1.94590.33817734681400.2806530833322667X-RAY DIFFRACTION99.08224497
1.9459-1.98560.2842441399521610.2518666081962627X-RAY DIFFRACTION99.5003568879
1.9856-2.02880.3391154325831440.2422331957332676X-RAY DIFFRACTION99.4708994709
2.0288-2.0760.2528596079531370.2303338984352666X-RAY DIFFRACTION99.6445076431
2.076-2.12790.2521888016371350.2115033559082696X-RAY DIFFRACTION99.6480112636
2.1279-2.18550.2501428611621340.2107972049382675X-RAY DIFFRACTION99.4336283186
2.1855-2.24980.2490705386111350.1973245760682676X-RAY DIFFRACTION99.5396600567
2.2498-2.32240.2187738507941360.1933349460412679X-RAY DIFFRACTION99.8226950355
2.3224-2.40540.2314918054611330.1921123997012725X-RAY DIFFRACTION99.7556719023
2.4054-2.50170.2275936492511220.1920600659462679X-RAY DIFFRACTION99.8573975045
2.5017-2.61550.2296062885641460.1909868889462684X-RAY DIFFRACTION99.8588567396
2.6155-2.75340.2173998836221250.1907121896612704X-RAY DIFFRACTION99.964664311
2.7534-2.92590.2545258155431590.1972494491492682X-RAY DIFFRACTION100
2.9259-3.15180.2056787698471670.1860047629242633X-RAY DIFFRACTION99.9642984648
3.1518-3.4690.2000115530781370.1774348561212719X-RAY DIFFRACTION100
3.469-3.97080.1998615863481510.1661131274972707X-RAY DIFFRACTION100
3.9708-5.00220.1764909328051300.1353858595422709X-RAY DIFFRACTION100
5.0022-54.0790.1991437041231390.1806430776482761X-RAY DIFFRACTION99.6906153317
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)
12.707980033980.723723341728-0.1128672132562.326086911570.1216397592542.06262874709-0.005498859260550.485868735131-0.0575266206105-0.2846906763020.108631709770.002989497681770.156391052171-0.204055047738-0.02488017252380.27784665238-0.0536611724428-0.00733777679090.385139939117-0.0180276637670.222437046599-2.0013511686331.0705931501-14.8922691761
23.14568130961.8249215561-0.5105258035322.65786752223-0.7632200755321.8151382374-0.0272330408084-0.02481135348980.1152562586070.1807237056680.03747466773780.1906043761990.0499405734712-0.295125931232-0.03096861672630.19513181301-0.007443135067480.01385142229750.271188913419-0.02609951711980.208944275592-2.3312619153835.9615287061-0.576721434618
32.04821095160.3056033014750.4633820960452.415943836790.5118536640582.82989041642-0.10794856884-0.03596742513790.6663826695660.209486281086-0.005094168257510.0515940359807-0.568905631388-0.2381940914280.07932550402820.402516166310.0485245031285-0.03902745541210.2873570232860.0207314523910.5106104177215.9098864348257.1681501636-2.65294660052
42.53170493022-0.272687110964-0.6343240230823.72934273479-1.236612620412.57318808658-0.1110760414720.179858630196-0.0221690964208-0.1733757533490.014009310792-0.2341776094050.4259931626850.04057120174050.1185550495820.196090625746-0.02648611327992.21444357153E-50.259489213495-0.05878835153390.1761666482369.6673243903631.7800066737-8.60563584157
52.045738537420.134721149418-0.7555445668782.86012188752-0.4363664189622.81053495078-0.0364058814632-0.635993413651-0.1148549850820.7009296699180.0319142602766-0.225145997170.2422089027150.2842411382310.0876855545840.4458379574650.0290473151373-0.08525750666190.4438218378520.00996625908690.25789096271420.127403945224.912531299124.6051571521
61.02267119693-0.948705603923-0.3928052745624.972399999570.1758825275971.84599798056-0.108310283359-0.1019581388410.01188561867680.08058112006220.0723695093792-0.3545870631830.154531269180.285283834750.006525877430590.212093212086-0.0265909013147-0.04597097617460.311806920092-0.03626647620920.23746789367922.916468878631.715850930710.5143004722
72.343365960810.993957562806-0.03255751219483.59976109707-0.1559955492372.48093057806-0.001286482092490.0502555952047-0.010818344899-0.0268538287956-0.0395572086625-0.604400099743-0.3478730364930.5097231271480.005589697579340.356246547539-0.134437770222-0.04299939611480.497781806365-0.0935417666470.5369552447728.596525325349.599313456211.0226021385
82.14720808957-0.170843946832-0.7830027296082.72740498315-0.3816179476661.756504295480.0313020139941-0.3691580408970.07060838680860.323810252504-0.08535148368240.1479743787270.170271521638-0.05032005534730.1030030076180.2840680491-0.0479104189317-0.03616884624560.331033367248-0.03902677064540.20908141760410.711726819331.540490213217.9641472127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 65 )
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 116 )
3X-RAY DIFFRACTION3chain 'A' and (resid 117 through 217 )
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 262 )
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 65 )
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 123 )
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 217 )
8X-RAY DIFFRACTION8chain 'B' and (resid 218 through 261 )

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