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- PDB-6fqk: GluA2(flop) S729C ligand binding core dimer bound to ZK200775 at ... -

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Basic information

Entry
Database: PDB / ID: 6fqk
TitleGluA2(flop) S729C ligand binding core dimer bound to ZK200775 at 1.98 Angstrom resolution
ComponentsGlutamate receptor 2,Glutamate 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 / 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
Chem-ZK1 / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.98010442598 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 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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)61,6524
Polymers60,8342
Non-polymers8192
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.696, 106.696, 100.394
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
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 20 or (resid 21...AA
2chain 'B'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
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-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid


Mass: 409.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15F3N3O6P / Comment: antagonist, medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Chloride, 20% PEG 3350, 10microM ZK200775.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / 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: 1.98→53.348 Å / Num. obs: 43458 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rpim(I) all: 0.024 / Rrim(I) all: 0.06 / Net I/σ(I): 17.2
Reflection shellResolution: 1.98→2.01 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimlessdata scaling
PHASERphasing
xia2data reduction
RefinementResolution: 1.98010442598→53.348 Å / SU ML: 0.340641349068 / Cross valid method: FREE R-VALUE / σ(F): 1.33437478937 / Phase error: 32.5202873569
RfactorNum. reflection% reflection
Rfree0.255734858832 2135 4.91561715746 %
Rwork0.217477194297 --
obs0.219368406855 43433 96.2056439109 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.3339272948 Å2
Refinement stepCycle: LAST / Resolution: 1.98010442598→53.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4031 0 54 300 4385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008863812309564164
X-RAY DIFFRACTIONf_angle_d1.153901792865615
X-RAY DIFFRACTIONf_chiral_restr0.0639502777473611
X-RAY DIFFRACTIONf_plane_restr0.00674080977653693
X-RAY DIFFRACTIONf_dihedral_angle_d7.430399417062499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9801-2.02620.424385994351380.4181477018082768X-RAY DIFFRACTION97.8780734254
2.0262-2.07680.5439179416991040.5098501240542391X-RAY DIFFRACTION83.4448160535
2.0768-2.1330.4326188729251420.3667425542742566X-RAY DIFFRACTION89.9368980405
2.133-2.19580.338243680831580.3066378645632803X-RAY DIFFRACTION99.4625461874
2.1958-2.26660.4629240736841050.4264269242642258X-RAY DIFFRACTION78.2709506459
2.2666-2.34760.3649668849921390.2975913451962823X-RAY DIFFRACTION99.2627345845
2.3476-2.44160.3292547933271580.2726175768462863X-RAY DIFFRACTION99.4731643069
2.4416-2.55280.3234814729331550.258745970992813X-RAY DIFFRACTION99.5305164319
2.5528-2.68730.3503724893511440.2640875355032788X-RAY DIFFRACTION97.8311644978
2.6873-2.85570.29273869411590.2484728395942842X-RAY DIFFRACTION99.6017258546
2.8557-3.07620.2759284995121330.2259984831132879X-RAY DIFFRACTION99.9004975124
3.0762-3.38570.2467124653691610.1937101599622843X-RAY DIFFRACTION100
3.3857-3.87550.1943159253661370.1828905747362868X-RAY DIFFRACTION99.3060145406
3.8755-4.88220.1870164248591770.1457525362742851X-RAY DIFFRACTION99.6708360764
4.8822-53.36730.173498800281250.154191648882942X-RAY DIFFRACTION99.8047510576
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)
13.755756171340.0317883451491-0.0608688840952.900878554880.08135065938613.02085922345-0.0478816148777-0.268443854059-0.1015114182350.2849534735290.132330613455-0.1348807713580.3230633407580.292887468204-0.06246561871150.2035654587110.0618531656307-0.01331642728160.2836758126420.02379738705380.1785481883273.3357837608531.44005467658.75232558855
22.02087422745-0.56651955154-0.2197461832624.67551123491-0.277814599732.75569693914-0.2298117223110.07608576063851.08923843406-0.578194276884-0.208496265850.0461136447283-0.8302548195960.5016668493280.1624072232120.528963454851-0.120398879388-0.1984981857060.3124912182490.05789233909720.780346193275-5.3268516920257.08784607482.05293997162
33.161975891641.376349300780.4712551973172.385327672530.5627539123482.37459562059-0.0372016778788-0.315842244520.3667665098940.127020339521-0.1579110924410.4071108041960.147295841718-0.1246635289780.1802461402650.205084587096-0.0188901828210.01543354377580.249144196746-0.02838586173770.224566939132-10.12814269836.5317599818.64355532675
42.57443238554-0.1773646638370.9608436186452.693079635990.5469564520182.56974198642-0.1829603871081.16299477474-0.140878014513-0.8725008291880.2733492175460.1415714815170.48963323076-0.0124640715022-0.1156795151170.576456795919-0.167977129554-0.05259638983990.666185412010.01008246841430.279168331437-19.60711031324.064729346-24.5433366245
52.673055600910.2052150406461.034267739242.84131082729-0.1968633434632.55047870746-0.3525630436050.333836252630.306463712096-0.1168475179650.2697734042680.3830361901110.249592466617-0.32358473226-0.1830717349980.210880728893-0.0323616301404-0.06057904513820.305180029140.08317719767840.261216508989-22.562950737131.225220887-10.7475917946
62.42247589812-0.8450712717881.122339752863.808132080030.3151944511453.65228196861-0.624244637150.06787529096090.9529631891750.0167092129106-0.08059079790990.662041981839-0.359443485237-0.6873225275450.1987991417540.3334407809420.0564826018618-0.2192413575730.5447359982260.08081764436770.835685654902-28.66952782248.8083646753-11.8866773074
73.214609094270.02534510243660.7333444234331.870459425630.6594457316382.03280058562-0.1326804777410.7228381283160.253132926316-0.4182512111750.181825598749-0.1671118500760.2833103383210.167720143985-0.001167659124530.299062533159-0.04120196989080.009363763097330.4349444743640.07859882859390.210027209281-10.332028035330.9486220496-18.2163746421
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 202 )
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 262 )
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 65 )
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 123 )
6X-RAY DIFFRACTION6chain 'B' and (resid 124 through 217 )
7X-RAY DIFFRACTION7chain 'B' and (resid 218 through 261 )

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