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- PDB-6q60: Structure of GluA2 ligand-binding domain (S1S2J) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6q60
TitleStructure of GluA2 ligand-binding domain (S1S2J) in complex with the agonist (S)-2-Amino-3-(2-methyl-5-hydroxy-2H-1,2,3-triazol-4-yl)propanoic acid at 1.55 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor / GluA2-S1S2 / ligand binding domain / agonist
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 / extracellularly glutamate-gated ion channel activity ...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 / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / 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 / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / 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 transmission, glutamatergic / synaptic membrane / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / establishment of protein localization / modulation of chemical synaptic transmission / 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 / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / 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-HJH / : / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMoellerud, S. / Temperini, P. / Kastrup, J.S.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Use of the 4-Hydroxytriazole Moiety as a Bioisosteric Tool in the Development of Ionotropic Glutamate Receptor Ligands.
Authors: Sainas, S. / Temperini, P. / Farnsworth, J.C. / Yi, F. / Mollerud, S. / Jensen, A.A. / Nielsen, B. / Passoni, A. / Kastrup, J.S. / Hansen, K.B. / Boschi, D. / Pickering, D.S. / Clausen, R.P. / Lolli, M.L.
History
DepositionDec 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)60,53925
Polymers58,5572
Non-polymers1,98223
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-82 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.344, 122.254, 47.351
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-737-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 20 or resid 22...
21(chain B and (resid 1 through 20 or resid 22...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 20 or resid 22...A1 - 20
121(chain A and (resid 1 through 20 or resid 22...A22 - 24
131(chain A and (resid 1 through 20 or resid 22...A26 - 42
141(chain A and (resid 1 through 20 or resid 22...A44 - 53
151(chain A and (resid 1 through 20 or resid 22...A78 - 106
161(chain A and (resid 1 through 20 or resid 22...A1 - 264
171(chain A and (resid 1 through 20 or resid 22...A157 - 163
181(chain A and (resid 1 through 20 or resid 22...A165 - 200
191(chain A and (resid 1 through 20 or resid 22...A203 - 2091
1101(chain A and (resid 1 through 20 or resid 22...A223 - 21
1111(chain A and (resid 1 through 20 or resid 22...A223 - 229
1121(chain A and (resid 1 through 20 or resid 22...A231 - 247
1131(chain A and (resid 1 through 20 or resid 22...A249 - 251
1141(chain A and (resid 1 through 20 or resid 22...A254 - 263
211(chain B and (resid 1 through 20 or resid 22...B1 - 20
221(chain B and (resid 1 through 20 or resid 22...B22 - 24
231(chain B and (resid 1 through 20 or resid 22...B26 - 42
241(chain B and (resid 1 through 20 or resid 22...B44 - 53
251(chain B and (resid 1 through 20 or resid 22...B78 - 106
261(chain B and (resid 1 through 20 or resid 22...B1 - 263
271(chain B and (resid 1 through 20 or resid 22...B157 - 163
281(chain B and (resid 1 through 20 or resid 22...B165 - 200
291(chain B and (resid 1 through 20 or resid 22...B203 - 2091
2101(chain B and (resid 1 through 20 or resid 22...B223 - 21
2111(chain B and (resid 1 through 20 or resid 22...B223 - 229
2121(chain B and (resid 1 through 20 or resid 22...B231 - 247
2131(chain B and (resid 1 through 20 or resid 22...B249 - 251
2141(chain B and (resid 1 through 20 or resid 22...B254 - 263

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Components

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Protein , 1 types, 2 molecules AB

#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: 29278.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions were replaced with a Gly-Thr linker (118-119). Sequence matches discontinously with the ...Details: The protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions were replaced with a Gly-Thr linker (118-119). Sequence matches discontinously with the reference database (413-527, 653-797). Residues 1-2 are cloning remnants.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

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Non-polymers , 6 types, 758 molecules

#2: Chemical ChemComp-HJH / (2~{S})-2-azanyl-3-(2-methyl-5-oxidanyl-1,2,3-triazol-4-yl)propanoic acid


Type: L-peptide linking / Mass: 186.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10N4O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG4000, 0.1 M lithium sulfate, 0.1 M phosphate-citrate, pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979988 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979988 Å / Relative weight: 1
ReflectionResolution: 1.55→44.15 Å / Num. obs: 83759 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 16.4 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Rsym value: 0.087 / Net I/av σ(I): 4.7 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.55-1.636.70.3681.6121030.1550.40.368100
1.63-1.736.70.272.1114200.1140.2940.27100
1.73-1.856.80.1962.9107640.0810.2120.196100
1.85-26.90.1453.9100470.060.1570.145100
2-2.196.80.1164.992700.0480.1260.116100
2.19-2.456.70.1035.684290.0420.1110.103100
2.45-2.836.70.0886.774700.0360.0950.088100
2.83-3.476.90.0757.763620.030.0810.075100
3.47-4.96.70.0638.950150.0260.0680.063100
4.9-44.1556.40.0518.928790.0230.0560.05199.5

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M5B

1m5b


Resolution: 1.55→44.155 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.28 / Phase error: 18.27
RfactorNum. reflection% reflection
Rfree0.1752 4173 5.01 %
Rwork0.148 --
obs0.1494 83371 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.04 Å2 / Biso mean: 24.3901 Å2 / Biso min: 9.02 Å2
Refinement stepCycle: final / Resolution: 1.55→44.155 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 236 751 5082
Biso mean--53.55 30.82 -
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094427
X-RAY DIFFRACTIONf_angle_d1.045973
X-RAY DIFFRACTIONf_chiral_restr0.064652
X-RAY DIFFRACTIONf_plane_restr0.007741
X-RAY DIFFRACTIONf_dihedral_angle_d14.6872716
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2804X-RAY DIFFRACTION5.651TORSIONAL
12B2804X-RAY DIFFRACTION5.651TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.56760.22961180.20162629274799
1.5676-1.58610.25011290.22599272899
1.5861-1.60540.20591320.19392570270299
1.6054-1.62570.19951270.18862599272699
1.6257-1.64710.23671440.17352580272499
1.6471-1.66970.22181130.17232622273599
1.6697-1.69350.22071580.16772587274599
1.6935-1.71880.18621220.17452605272799
1.7188-1.74570.20641400.162326442784100
1.7457-1.77430.1871390.15242586272599
1.7743-1.80490.20561310.15262598272999
1.8049-1.83770.17131290.159226342763100
1.8377-1.87310.20931310.156926382769100
1.8731-1.91130.21571570.155926022759100
1.9113-1.95290.19721440.154626202764100
1.9529-1.99830.18521350.153426312766100
1.9983-2.04830.18841600.150226112771100
2.0483-2.10360.17371460.140526172763100
2.1036-2.16550.16021340.139126462780100
2.1655-2.23540.15691380.133226412779100
2.2354-2.31530.16661400.13426402780100
2.3153-2.4080.17381270.134326642791100
2.408-2.51760.18051410.144126662807100
2.5176-2.65030.1711450.141826462791100
2.6503-2.81640.18731310.14226802811100
2.8164-3.03380.17381430.146526812824100
3.0338-3.3390.1521610.141726732834100
3.339-3.82190.15731510.137927022853100
3.8219-4.81420.14871510.123927382889100
4.8142-44.17270.17571560.1782849300599
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)
11.29720.0430.07572.8936-0.47092.1448-0.03610.0199-0.0767-0.11660.03450.00940.1138-0.0374-0.00490.11710.00170.00820.1086-0.00410.119229.835320.7421-32.9846
23.79340.18850.73141.87780.08072.99220.01050.1122-0.0586-0.08460.0102-0.29210.11820.4049-0.02070.11710.05080.02650.1226-0.00630.122242.129529.4474-39.066
30.42650.11240.08430.3273-0.22592.2961-0.019-0.03730.0226-0.0059-0.02940.0001-0.01340.1240.03870.11650.01990.01540.12890.0010.149338.526737.1569-28.0792
41.9450.3156-0.0612.9297-0.63272.57850.0027-0.08510.031-0.0174-0.083-0.2741-0.10730.52750.05270.1114-0.00840.01230.2470.00350.149349.163737.3921-18.497
51.0512-1.42551.00025.862-6.2088.9477-0.0863-0.1179-0.02820.1035-0.04550.13890.06970.09950.13410.13020.00780.0340.166-0.01630.169738.42334.9326-12.5154
62.7684-0.9615-1.42851.92250.36445.99620.00730.26950.0192-0.118-0.00590.0283-0.0138-0.15380.01520.10570.0051-0.00740.05340.00980.119427.107737.2395-38.045
72.9357-2.50433.96153.5932-4.34898.9168-0.0802-0.443-0.03870.21950.2530.08290.0638-0.551-0.2020.1841-0.00630.03990.1508-0.00070.160824.320428.7416-17.7927
81.6561-0.0471-0.35291.344-0.34451.76990.0386-0.01660.1032-0.0220.0012-0.0664-0.17440.0806-0.05540.1245-0.00920.01180.0979-0.01730.136729.668768.5266-32.7952
91.8271-0.31-0.70741.3041-0.0852.5950.06620.12280.0378-0.1150.00940.1859-0.0653-0.2978-0.07350.13510.0346-0.01160.12380.00790.146117.195559.8525-39.1715
100.25290.1095-0.39640.58640.10871.94960.0036-0.0076-0.01130.00730.01-0.01420.0006-0.0081-0.00780.10780.0125-0.0160.1053-0.00030.134220.607552.2307-28.1751
112.6060.6978-1.03514.67370.53153.2724-0.0930.0863-0.08050.0581-0.04180.27010.2746-0.30440.08130.1001-0.029-0.02320.1464-0.00040.18968.235447.3713-20.1519
122.94080.3196-0.47822.38251.16561.7168-0.0472-0.00550.0210.0194-0.00790.70410.1118-0.33290.06810.1078-0.0351-0.01950.17640.01510.23373.714449.8649-21.2951
133.69791.5183-1.62154.5784-0.31135.24950.1220.04080.18060.3482-0.07670.4514-0.1945-0.4246-0.12060.13420.01290.02230.1306-0.00730.18410.278361.8092-13.2119
140.642-0.2716-0.74690.5540.41651.29930.0089-0.08720.05230.02970.0678-0.0859-0.00110.1385-0.07540.13810.0056-0.01460.1361-0.00530.157727.884955.6825-22.939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 79 )A48 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 123 )A80 - 123
4X-RAY DIFFRACTION4chain 'A' and (resid 124 through 202 )A124 - 202
5X-RAY DIFFRACTION5chain 'A' and (resid 203 through 217 )A203 - 217
6X-RAY DIFFRACTION6chain 'A' and (resid 218 through 243 )A218 - 243
7X-RAY DIFFRACTION7chain 'A' and (resid 244 through 264 )A244 - 264
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 47 )B1 - 47
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 79 )B48 - 79
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 123 )B80 - 123
11X-RAY DIFFRACTION11chain 'B' and (resid 124 through 152 )B124 - 152
12X-RAY DIFFRACTION12chain 'B' and (resid 153 through 173 )B153 - 173
13X-RAY DIFFRACTION13chain 'B' and (resid 174 through 187 )B174 - 187
14X-RAY DIFFRACTION14chain 'B' and (resid 188 through 263 )B188 - 263

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