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- PDB-3b7d: Crystal structure of the GLUR2 ligand binding core (HS1S2J) in co... -

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Basic information

Entry
Database: PDB / ID: 3b7d
TitleCrystal structure of the GLUR2 ligand binding core (HS1S2J) in complex with CNQX at 2.5 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / S1S2 / CNQX / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / Cell junction / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Palmitate / Phosphorylation / Postsynaptic cell membrane / Receptor / RNA editing / Synapse / Transmembrane / Transport
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
Chem-CNI / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHays, F.A. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Science / Year: 2007
Title: TARP auxiliary subunits switch AMPA receptor antagonists into partial agonists.
Authors: Menuz, K. / Stroud, R.M. / Nicoll, R.A. / Hays, F.A.
History
DepositionOct 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_ref_seq_dif / struct_site
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.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
C: Glutamate receptor 2
D: Glutamate receptor 2
E: Glutamate receptor 2
F: Glutamate receptor 2
G: Glutamate receptor 2
H: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,46216
Polymers232,6208
Non-polymers1,8418
Water10,215567
1
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6154
Polymers58,1552
Non-polymers4602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
MethodPISA
2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6154
Polymers58,1552
Non-polymers4602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
MethodPISA
3
E: Glutamate receptor 2
F: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6154
Polymers58,1552
Non-polymers4602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
MethodPISA
4
G: Glutamate receptor 2
H: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6154
Polymers58,1552
Non-polymers4602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.582, 97.631, 100.970
Angle α, β, γ (deg.)81.85, 89.08, 77.89
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
12F
22D
13H
23D
14C
24A
15E
25A
35E
45A
55E
65A
16G
26A

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRCYSCYS1BB5 - 2615 - 261
211THRTHRCYSCYS1DD5 - 2615 - 261
112THRTHRCYSCYS1FF5 - 2615 - 261
212THRTHRCYSCYS1DD5 - 2615 - 261
113THRTHRCYSCYS1HH5 - 2615 - 261
213THRTHRCYSCYS1DD5 - 2615 - 261
114THRTHRCYSCYS1CC5 - 2615 - 261
214THRTHRCYSCYS1AA5 - 2615 - 261
115THRTHRALAALA1EE5 - 635 - 63
215THRTHRALAALA1AA5 - 635 - 63
325ASPASPCYSCYS1EE65 - 26165 - 261
425ASPASPCYSCYS1AA65 - 26165 - 261
535ARGARGARGARG3EE6464
635ARGARGARGARG3AA6464
116THRTHRCYSCYS1GG5 - 2615 - 261
216THRTHRCYSCYS1AA5 - 2615 - 261

NCS ensembles :
ID
1
2
3
4
5
6
DetailsAuthors state that the biological unit of this protein is unknown.

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Components

#1: Protein
Glutamate receptor 2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / AMPA-selective glutamate receptor 2


Mass: 29077.553 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: modified pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: P19491
#2: Chemical
ChemComp-CNI / 7-nitro-2,3-dioxo-2,3-dihydroquinoxaline-6-carbonitrile


Mass: 230.137 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H2N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growpH: 6.5
Details: 40 mM Sodium citrate, 10 mM Ammonium sulfate, 1% PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2007 / Details: KOHZU: DOUBLE CRYSTAL SI(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.4→39.9 Å / Num. obs: 92349 / % possible obs: 96.8 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.87

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FTJ
Resolution: 2.5→39.9 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.875 / SU B: 21.958 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.79 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28313 4133 5 %RANDOM
Rwork0.25455 ---
obs0.25598 82433 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.383 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å2-0.15 Å23.41 Å2
2---1.93 Å20.03 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15989 0 136 567 16692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02216446
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211254
X-RAY DIFFRACTIONr_angle_refined_deg0.8791.98222175
X-RAY DIFFRACTIONr_angle_other_deg0.7733.00127519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09452059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61924.326638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.743153028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1291577
X-RAY DIFFRACTIONr_chiral_restr0.0490.22443
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0218058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023211
X-RAY DIFFRACTIONr_nbd_refined0.1730.22799
X-RAY DIFFRACTIONr_nbd_other0.1820.210871
X-RAY DIFFRACTIONr_nbtor_refined0.170.27942
X-RAY DIFFRACTIONr_nbtor_other0.0810.28401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2597
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.2132
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1731.510544
X-RAY DIFFRACTIONr_mcbond_other0.0261.54257
X-RAY DIFFRACTIONr_mcangle_it0.306216365
X-RAY DIFFRACTIONr_scbond_it0.39637036
X-RAY DIFFRACTIONr_scangle_it0.6724.55809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B3385tight positional0.010.05
2F3398tight positional0.010.05
3H3392tight positional0.010.05
4C3374tight positional0.010.05
5E3325tight positional0.010.05
6G3364tight positional0.010.05
5E18loose positional1.345
1B3385tight thermal0.020.5
2F3398tight thermal0.020.5
3H3392tight thermal0.020.5
4C3374tight thermal0.070.5
5E3325tight thermal0.070.5
6G3364tight thermal0.070.5
5E18loose thermal1.4510
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 297 -
Rwork0.341 5710 -
obs--95.68 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.6698-0.2516-1.23132.91511.27893.0621-0.13510.4236-0.35830.1145-0.03640.49690.1001-0.34860.1715-0.13150.0276-0.03320.0764-0.06160.156-34.02288.0569-45.8162
24.8365-1.6719-1.53684.12190.55378.191-0.2057-0.52610.2260.46530.5502-0.12380.86010.5885-0.34460.19520.07430.0590.0884-0.09860.0232-25.295423.4426-26.4138
31.1724-1.3051-1.26383.36881.61282.90010.16910.26280.1427-0.1614-0.0529-0.0243-0.2904-0.144-0.1162-0.0033-0.00130.0140.1160.0120.1417-26.258618.9994-46.2587
41.26710.2405-1.02223.1566-0.34781.6806-0.1231-0.1049-0.1290.1830.0509-0.13780.17170.17680.0722-0.06370.0341-0.0720.1067-0.0220.0906-1.70484.0299-46.3568
51.22570.3322-1.00422.0347-1.01472.4357-0.0462-0.05350.08180.0930.104-0.07350.0170.0173-0.0579-0.00160.0281-0.04050.059-0.05080.1172-3.394914.8142-50.4097
63.2190.2097-0.85673.2871-0.76442.2378-0.2694-0.4134-0.51210.02770.1489-0.45150.30280.29290.1205-0.07220.04070.03670.1340.03130.1774-10.63-47.4613-46.9183
74.3323-0.232-0.99762.96380.75116.82320.33570.24680.4364-0.33470.1293-0.1664-0.2416-0.4585-0.465-0.0127-0.0060.05130.04370.05530.0393-11.2786-28.4168-65.734
82.95881.7445-1.93171.8757-0.97862.9480.0881-0.41870.15420.10410.0218-0.1945-0.13090.2462-0.1099-0.00390.03250.01090.1057-0.03910.1778-13.7987-34.0939-46.2484
91.27070.0069-0.62573.14270.82781.6529-0.01230.1874-0.0279-0.0282-0.02630.19260.0798-0.20030.0386-0.0861-0.0165-0.05570.10910.0290.0711-41.6785-37.0341-46.5366
101.0262-0.0683-0.65852.26651.3882.72480.01140.13440.11690.07120.11740.1354-0.02890.0619-0.1288-0.0217-0.0388-0.00830.07230.03770.1199-35.7002-28.1119-42.6629
111.5134-0.0194-0.15183.53620.89123.7516-0.08350.10560.2257-0.69910.13630.1347-0.7746-0.4043-0.05280.39880.04810.04580.0990.00380.03715.7527-10.2723-12.8949
126.3518-0.4702-1.64833.18420.29936.9787-0.1483-0.34850.3990.09780.2845-0.15070.54810.4386-0.13620.08210.04020.03390.033-0.0601-0.006820.7103-31.8972-15.5799
131.2911-0.156-0.80852.08232.25973.4274-0.0123-0.0098-0.0359-0.0849-0.08420.21070.0327-0.39610.09660.2709-0.00450.05250.12560.0490.07524.6123-22.6969-7.1277
141.13931.2788-0.45723.1148-0.32082.04940.0708-0.0484-0.01310.30760.0076-0.1742-0.19540.2076-0.07840.2210.00040.03360.1196-0.05260.096116.6557-16.030817.117
151.9881.3672-0.87671.8146-0.73972.18480.00350.1184-0.0490.09150.0536-0.13980.09310.0231-0.05720.173-0.01570.02810.0779-0.07250.11469.6242-24.829615.0932
161.54710.7401-0.12633.4465-1.28913.50530.00970.04950.05690.7769-0.0989-0.1833-0.50530.77580.08920.2969-0.1176-0.03350.18450.0062-0.012428.343734.860119.3326
174.47430.0319-1.65863.1905-0.45975.642-0.11570.33750.2243-0.06960.17010.1520.4623-0.4562-0.05440.063-0.06240.00390.09570.0325-0.04145.461620.988422.2682
181.74960.4808-1.52311.9036-1.54623.3891-0.21490.0704-0.2122-0.0358-0.0123-0.19770.38960.35180.22710.2394-0.0188-0.00260.1337-0.02140.045623.835423.151413.5468
191.1329-0.3425-0.6983.23470.30052.20920.00350.14470.055-0.19250.02670.2318-0.1568-0.1896-0.03020.1022-0.0436-0.00640.13810.03510.079515.467334.0152-10.8759
200.9615-0.592-0.82372.63350.62712.2402-0.08270.0078-0.06220.02610.08510.14930.0991-0.1346-0.00240.1646-0.03360.03980.08420.04510.107218.279123.1322-8.7437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1185 - 118
2X-RAY DIFFRACTION2AA119 - 178119 - 178
3X-RAY DIFFRACTION3AA179 - 261179 - 261
4X-RAY DIFFRACTION4BB5 - 1345 - 134
5X-RAY DIFFRACTION5BB135 - 261135 - 261
6X-RAY DIFFRACTION6CC5 - 1155 - 115
7X-RAY DIFFRACTION7CC116 - 182116 - 182
8X-RAY DIFFRACTION8CC183 - 261183 - 261
9X-RAY DIFFRACTION9DD5 - 1345 - 134
10X-RAY DIFFRACTION10DD135 - 261135 - 261
11X-RAY DIFFRACTION11EE5 - 1155 - 115
12X-RAY DIFFRACTION12EE116 - 182116 - 182
13X-RAY DIFFRACTION13EE183 - 261183 - 261
14X-RAY DIFFRACTION14FF5 - 1345 - 134
15X-RAY DIFFRACTION15FF135 - 261135 - 261
16X-RAY DIFFRACTION16GG5 - 1155 - 115
17X-RAY DIFFRACTION17GG116 - 182116 - 182
18X-RAY DIFFRACTION18GG183 - 261183 - 261
19X-RAY DIFFRACTION19HH5 - 1345 - 134
20X-RAY DIFFRACTION20HH135 - 261135 - 261

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