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- PDB-6q54: Structure of GluA2 ligand-binding domain (S1S2J) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6q54
TitleStructure of GluA2 ligand-binding domain (S1S2J) in complex with the agonist (S)-2-Amino-3-(1-ethyl-4-hydroxy-1H-1,2,3-triazol-5-yl)propanoic acid at 1.4 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptor / AMPA receptor / ligand-binding domain / GluA2-S1S2 / GluA2 / GluR2 / 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 / 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
CITRIC ACID / Chem-HJ8 / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 7, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)61,01328
Polymers58,5572
Non-polymers2,45526
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-135 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.331, 121.738, 47.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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: Native GluA2 is a membrane protein. The protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions were genetically removed and replaced with a Gly-Thr ...Details: Native GluA2 is a membrane protein. The protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with reference database (413-527,653-797). Residues 1-2 are cloning remnants.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

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Non-polymers , 9 types, 720 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HJ8 / (2~{S})-2-azanyl-3-(3-ethyl-5-oxidanyl-1,2,3-triazol-4-yl)propanoic acid


Mass: 200.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12N4O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#8: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Li
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG4000, 0.3 M lithium sulfate, 0.1 M phosphate-citrate

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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: 1.4→45.59 Å / Num. obs: 112106 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 14.33 Å2 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Rsym value: 0.053 / Net I/av σ(I): 8.3 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.4-1.486.70.4581.6161950.1890.4960.45899.9
1.48-1.576.80.2992.4152900.1230.3240.29999.9
1.57-1.676.80.2013.6144410.0830.2180.201100
1.67-1.816.80.1434.9134430.0590.1550.143100
1.81-1.986.70.0967.1124440.040.1040.096100
1.98-2.216.60.06410.1112550.0270.070.064100
2.21-2.5670.05212.199970.0210.0570.052100
2.56-3.136.90.04114.385260.0170.0440.041100
3.13-4.436.80.03117.966680.0130.0340.031100
4.43-45.596.50.03215.638470.0130.0340.03299.7

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Processing

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

1m5b


Resolution: 1.4→43.954 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0.63 / Phase error: 16.11
RfactorNum. reflection% reflection
Rfree0.1633 5522 4.93 %
Rwork0.1442 --
obs0.1451 112001 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.49 Å2 / Biso mean: 22.2411 Å2 / Biso min: 7.34 Å2
Refinement stepCycle: final / Resolution: 1.4→43.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 245 703 5043
Biso mean--37.59 29.27 -
Num. residues----527
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014454
X-RAY DIFFRACTIONf_angle_d1.1496014
X-RAY DIFFRACTIONf_chiral_restr0.086651
X-RAY DIFFRACTIONf_plane_restr0.008748
X-RAY DIFFRACTIONf_dihedral_angle_d17.8361716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.41590.2461840.21734803664
1.4159-1.43260.25371860.207135143700
1.4326-1.450.24561570.203335263683
1.45-1.46840.23081610.185135183679
1.4684-1.48770.18261830.174534843667
1.4877-1.50810.19231970.172834843681
1.5081-1.52960.18721950.169535133708
1.5296-1.55250.1731990.15534903689
1.5525-1.57670.17081830.152935203703
1.5767-1.60260.18471930.153535043697
1.6026-1.63020.16511970.149635143711
1.6302-1.65990.1411570.145535073664
1.6599-1.69180.15321790.148335673746
1.6918-1.72630.17971700.150435243694
1.7263-1.76390.16931950.14535153710
1.7639-1.80490.16661730.145435353708
1.8049-1.850.15031730.147135553728
1.85-1.90010.16192150.137135183733
1.9001-1.9560.13751820.135635293711
1.956-2.01910.15981790.134135423721
2.0191-2.09130.14711780.132935523730
2.0913-2.1750.1391970.129535733770
2.175-2.2740.17181950.122535283723
2.274-2.39390.15571830.134335653748
2.3939-2.54380.17612020.136435573759
2.5438-2.74020.16611890.14235993788
2.7402-3.01590.1691770.150136113788
3.0159-3.45220.15281880.142536273815
3.4522-4.34880.13671820.12936893871
4.3488-43.97620.18031730.157538394012
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)
10.345-0.20760.18470.3821-0.010.3184-0.01870.0175-0.00090.0336-0.0176-0.0073-0.0889-0.044200.1639-0.0009-0.00080.1160.00450.1237-19.362640.7962-14.3168
20.1035-0.1182-0.24980.06580.22510.7084-0.0078-0.07930.02960.04070.0323-0.0314-0.13710.14590.00550.1274-0.0366-0.00560.15130.00040.1405-6.98331.9059-8.1751
30.2982-0.22590.03740.1442-0.1720.2048-0.00420.0583-0.00940.0221-0.02820.010.00340.0283-0.01220.1118-0.0206-0.00630.13360.00830.1246-10.529324.356-18.9711
40.88030.08440.16340.7027-0.46030.7550.11290.0597-0.03540.0504-0.1329-0.08570.08970.2634-0.00060.09960.023-0.00030.18960.00920.1543.143220.005-26.3005
50.15230.06540.04240.0440.03160.05560.14020.08870.3688-0.008-0.1575-0.0797-0.26970.2552-0.10940.1791-0.01280.03540.26870.07730.17370.102133.6799-33.6894
60.1419-0.04530.06240.2319-0.12250.38540.04480.08370.0055-0.0235-0.03240.0874-0.0063-0.0169-00.1323-0.00290.00350.16590.01620.1304-10.681728.2019-32.6815
70.22070.10660.10290.4055-0.13160.1302-0.0036-0.0425-0.04710.05280.00620.0153-0.0067-0.0141-00.1059-0.01020.00390.12550.00510.1252-22.200124.1827-9.1823
80.1181-0.09270.00280.1242-0.06670.06160.00330.04-0.0698-0.0948-0.01240.0287-0.1058-0.044800.1671-0.0004-0.0070.150.00660.1387-24.749732.8034-29.589
90.3854-0.0349-0.33550.2728-0.03870.2292-0.02740.0045-0.01890.02020.0144-0.01920.1340.071200.1908-0.0099-0.0260.1326-0.00290.1367-22.3609-6.8741-14.3676
100.11790.05910.09760.10880.04330.15640.04710.046-0.05730.09960.0177-0.13920.06980.08050.02620.1868-0.0027-0.04450.1269-0.00880.1601-17.3958-7.521-14.7049
110.1130.10940.05660.12240.12020.3050.00980.0295-0.05050.0943-0.01080.03290.0945-0.02250.04420.147-0.0363-0.03010.11180.01670.1285-28.3206-1.2064-9.3783
120.0990.07460.12170.53810.14320.14990.05960.03860.02250.12040.0276-0.07770.1604-0.21430.03870.1331-0.03320.00290.17730.02130.1141-37.14015.3195-6.0361
13-0.0457-0.13270.09940.40380.35090.2705-0.0144-0.00730.0065-0.00570.0037-0.0387-0.0022-0.0042-00.1237-0.025-0.00370.12120.00940.1234-28.8879.4485-18.432
140.4319-0.25850.12930.45550.19780.1830.0485-0.10740.0223-0.0742-0.07310.1128-0.1099-0.14460.00110.14010.001-0.02540.1584-0.0040.1543-41.233814.076-26.8061
150.123-0.10810.00430.23270.33880.54290.07420.0108-0.0336-0.0726-0.09230.1452-0.1135-0.0910.02010.1235-0.0062-0.01980.1554-0.00450.1906-45.656611.3063-25.7139
160.1815-0.06-0.02970.1699-0.00110.22910.1015-0.0813-0.1529-0.0773-0.10470.09740.1411-0.1409-0.05310.1557-0.0127-0.04080.1394-0.01130.1461-39.0792-0.4132-33.7735
170.25280.0640.13660.50070.2550.19370.02890.0142-0.0159-0.03920.0028-0.0616-0.00740.0127-00.1203-0.0178-0.00410.11730.00590.1298-24.28547.682-22.6056
180.1741-0.09010.01040.06430.03280.00850.00860.2521-0.08810.01130.15110.01520.02830.133400.174-0.0087-0.00430.1849-0.02770.1862-14.89651.4733-28.3577
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 173 )A124 - 173
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 187 )A174 - 187
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 217 )A188 - 217
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 243 )A218 - 243
8X-RAY DIFFRACTION8chain 'A' and (resid 244 through 264 )A244 - 264
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 22 )B1 - 22
10X-RAY DIFFRACTION10chain 'B' and (resid 23 through 47 )B23 - 47
11X-RAY DIFFRACTION11chain 'B' and (resid 48 through 65 )B48 - 65
12X-RAY DIFFRACTION12chain 'B' and (resid 66 through 79 )B66 - 79
13X-RAY DIFFRACTION13chain 'B' and (resid 80 through 123 )B80 - 123
14X-RAY DIFFRACTION14chain 'B' and (resid 124 through 152 )B124 - 152
15X-RAY DIFFRACTION15chain 'B' and (resid 153 through 173 )B153 - 173
16X-RAY DIFFRACTION16chain 'B' and (resid 174 through 187 )B174 - 187
17X-RAY DIFFRACTION17chain 'B' and (resid 188 through 243 )B188 - 243
18X-RAY DIFFRACTION18chain 'B' and (resid 244 through 263 )B244 - 263

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