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- PDB-5buu: Crystal structure of the GluA2 ligand-binding domain (L483Y-N754S... -

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Basic information

Entry
Database: PDB / ID: 5buu
TitleCrystal structure of the GluA2 ligand-binding domain (L483Y-N754S) in complex with glutamate and BPAM-321 at 2.07 A resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor ligand-binding domain / GluA2 L483Y-N754S / BPAM-321 positive allosteric modulation
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-4V6 / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å
AuthorsLarsen, A.P. / Tapken, D. / Frydenvang, K. / Kastrup, J.S.
Citation
Journal: Acs Chem Neurosci / Year: 2016
Title: Synthesis and Pharmacology of Mono-, Di-, and Trialkyl-Substituted 7-Chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides Combined with X-ray Structure Analysis to Understand the ...Title: Synthesis and Pharmacology of Mono-, Di-, and Trialkyl-Substituted 7-Chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-Dioxides Combined with X-ray Structure Analysis to Understand the Unexpected Structure-Activity Relationship at AMPA Receptors.
Authors: Larsen, A.P. / Francotte, P. / Frydenvang, K. / Tapken, D. / Goffin, E. / Fraikin, P. / Caignard, D.H. / Lestage, P. / Danober, L. / Pirotte, B. / Kastrup, J.S.
#1: Journal: J. Med. Chem. / Year: 2013
Title: Synthesis, pharmacological and structural characterization, and thermodynamic aspects of GluA2-positive allosteric modulators with a 3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide scaffold.
Authors: Norholm, A.B. / Francotte, P. / Olsen, L. / Krintel, C. / Frydenvang, K. / Goffin, E. / Challal, S. / Danober, L. / Botez-Pop, I. / Lestage, P. / Pirotte, B. / Kastrup, J.S.
#2: Journal: Biochemistry / Year: 2009
Title: Probing the allosteric modulator binding site of GluR2 with thiazide derivatives.
Authors: Ptak, C.P. / Ahmed, A.H. / Oswald, R.E.
History
DepositionJun 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 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,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,09616
Polymers58,4892
Non-polymers1,60614
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-73 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.209, 122.270, 47.652
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,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: 29244.678 Da / Num. of mol.: 2 / Fragment: UNP residues 413-527,UNP residues 653-796 / Mutation: L483Y, N754S,L483Y, N754S
Source method: isolated from a genetically manipulated source
Details: Ligand-binding domain, UNP residues 392-506 and 632-775 connected by a GT linker (numbering without signal peptide)
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19491

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Non-polymers , 5 types, 289 molecules

#2: Chemical ChemComp-4V6 / (3R)-7-chloro-2,3,4-trimethyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide / BPAM-321


Mass: 260.740 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13ClN2O2S
#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15.2 % PEG4000, 0.2 M ammonium-sulfate, 0.1 M phosphate-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.07→47.652 Å / Num. all: 36199 / Num. obs: 36199 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.45 Å2 / Rpim(I) all: 0.032 / Rrim(I) all: 0.065 / Rsym value: 0.057 / Net I/av σ(I): 8.977 / Net I/σ(I): 13.9 / Num. measured all: 147486
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.07-2.184.10.3322.12137551840.180.3324.1100
2.18-2.314.10.2822.32011849150.1550.2825.3100
2.31-2.474.10.174.31917846330.0920.176.8100
2.47-2.674.10.11661794643560.0630.1169100
2.67-2.934.10.0778.71643739950.0430.07712.5100
2.93-3.274.10.05213.21491436340.0290.05217.2100
3.27-3.7840.04115.11312932420.0230.04125100
3.78-4.6340.027211112927660.0150.02731.5100
4.63-6.553.90.02221.4862021920.0130.02229.3100
6.55-47.6523.60.0310.8464012820.0190.0330.599.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.63 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.65 Å
Translation2.5 Å47.65 Å

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Processing

Software
NameClassification
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tkd, molA

3tkd


Resolution: 2.07→47.652 Å / FOM work R set: 0.8118 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 1793 5 %Random selection
Rwork0.2037 34101 --
obs0.206 35894 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.79 Å2 / Biso mean: 44.3 Å2 / Biso min: 10.31 Å2
Refinement stepCycle: final / Resolution: 2.07→47.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 97 275 4396
Biso mean--43.43 42.12 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034241
X-RAY DIFFRACTIONf_angle_d0.6995718
X-RAY DIFFRACTIONf_chiral_restr0.047624
X-RAY DIFFRACTIONf_plane_restr0.003706
X-RAY DIFFRACTIONf_dihedral_angle_d13.0321619
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.1260.29411470.243125612708100
2.126-2.18850.25881230.233626292752100
2.1885-2.25920.46081180.3942484260295
2.2592-2.33990.29611410.28332489263096
2.3399-2.43360.27441330.222125972730100
2.4336-2.54440.30041330.219126422775100
2.5444-2.67850.27261570.220426122769100
2.6785-2.84630.28881320.212926022734100
2.8463-3.0660.25531400.213626472787100
3.066-3.37450.2531450.190626422787100
3.3745-3.86260.2021440.180426572801100
3.8626-4.86570.19451370.148827152852100
4.8657-47.66460.21761430.18162824296799
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)
13.4884-0.48390.48443.79380.0932.25780.24960.04440.48890.2635-0.05650.3884-0.6345-0.3001-0.12230.32150.04480.09320.18740.04030.2934-29.95296.61589.8577
21.52320.0167-0.65832.09150.35724.26220.113-0.22120.04420.17940.0135-0.1741-0.18320.3218-0.11790.2026-0.017-0.02320.1640.00890.2166-17.9023-7.05869.3578
34.2877-0.6053-0.82974.9926-1.08973.1391-0.0652-0.1276-0.0966-0.26510.0113-0.75840.15530.36990.05320.1836-0.00470.02690.18890.00190.3541-7.445-10.721-4.551
46.7394-0.6513-1.99934.7512-2.83466.6386-0.08410.35230.2182-0.70660.32580.04180.0417-0.5213-0.21590.3491-0.0753-0.02930.1853-0.01710.2407-18.0484-2.7015-10.7813
52.66690.0693-0.55692.7765-0.72063.1125-0.09180.1187-0.050.02160.11850.4332-0.1443-0.3286-0.03880.195-0.02060.010.19880.03380.2911-31.8458-8.16356.5162
66.9945-1.431-4.83861.50990.23383.85690.79570.0848-0.43230.4594-0.3917-0.1316-1.063-1.4075-0.25750.6974-0.040.01410.87080.12630.4951-31.36262.1064-11.6548
73.5413-0.7583-0.02094.07680.43162.8413-0.1174-0.094-0.59460.33360.09450.09430.4471-0.07640.00040.4077-0.07180.04060.18870.05120.2109-33.6495-37.304510.8867
83.951-0.9264-1.17612.6490.48131.4336-0.10840.2904-0.01010.01130.02720.2360.2175-0.5703-0.01170.2329-0.07570.03210.32520.00530.1886-40.0202-24.27726.325
94.761-1.04670.76092.21671.17071.96210.18711.4729-0.2726-0.3182-0.80810.82670.1749-1.01030.53380.4101-0.09890.00820.9315-0.20920.5387-49.6002-24.9788-4.8694
104.1042-1.0424-0.49082.90411.00442.8858-0.07610.4760.1497-0.08790.0442-0.13990.3532-0.2129-0.02660.2681-0.10260.06240.22430.01890.1698-29.1394-26.30082.877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 392:444)A392 - 444
2X-RAY DIFFRACTION2(chain A and resid 445:632)A445 - 632
3X-RAY DIFFRACTION3(chain A and resid 633:694)A633 - 694
4X-RAY DIFFRACTION4(chain A and resid 695:722)A695 - 722
5X-RAY DIFFRACTION5(chain A and resid 723:767)A723 - 767
6X-RAY DIFFRACTION6(chain A and resid 768:774)A768 - 774
7X-RAY DIFFRACTION7(chain B and resid 393:459)B393 - 459
8X-RAY DIFFRACTION8(chain B and resid 460:637)B460 - 637
9X-RAY DIFFRACTION9(chain B and resid 638:715)B638 - 715
10X-RAY DIFFRACTION10(chain B and resid 716:769)B716 - 769

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