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- PDB-6hcc: STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-N775S) IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 6hcc
TitleSTRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM02 AT 1.6 A RESOLUTION.
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / ampa receptor / gluA2 / ligand-binding domain / glua2-S1S2J-N775S / signaling protein / positive allosteric modulator
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / kainate selective glutamate receptor activity ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / immunoglobulin binding / asymmetric synapse / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / response to fungicide / regulation of synaptic transmission, glutamatergic / glutamate-gated receptor activity / cytoskeletal protein binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / somatodendritic compartment / ionotropic glutamate receptor binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / PDZ domain binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / protein tetramerization / synaptic membrane / establishment of protein localization / postsynaptic density membrane / modulation of chemical synaptic transmission / cerebral cortex development / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle membrane / synaptic vesicle / signaling receptor activity / presynapse / 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
ACETATE ION / Chem-FXW / GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.617 Å
AuthorsLaulumaa, S. / Hansen, K.V. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Crystal Structures of Potent Dimeric Positive Allosteric Modulators at the Ligand-Binding Domain of the GluA2 Receptor.
Authors: Laulumaa, S. / Hansen, K.V. / Masternak, M. / Drapier, T. / Francotte, P. / Pirotte, B. / Frydenvang, K. / Kastrup, J.S.
History
DepositionAug 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 1.2Oct 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)60,95226
Polymers58,5032
Non-polymers2,44924
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-82 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.979, 121.967, 47.395
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
11A-720-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:12 or resseq 14:20 or (resid...
21(chain B and (resseq 5:12 or resseq 14:20 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 5:12 or resseq 14:20 or (resid...A5 - 12
121(chain A and (resseq 5:12 or resseq 14:20 or (resid...A14 - 20
131(chain A and (resseq 5:12 or resseq 14:20 or (resid...A0
141(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
151(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
161(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
171(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
181(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
191(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
1101(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
1111(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
1121(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
1131(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
1141(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
1151(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
1161(chain A and (resseq 5:12 or resseq 14:20 or (resid...A1 - 264
211(chain B and (resseq 5:12 or resseq 14:20 or (resid...B5 - 12
221(chain B and (resseq 5:12 or resseq 14:20 or (resid...B14 - 20
231(chain B and (resseq 5:12 or resseq 14:20 or (resid...B0
241(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
251(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
261(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
271(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
281(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
291(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
2101(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
2111(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
2121(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
2131(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
2141(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
2151(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264
2161(chain B and (resseq 5:12 or resseq 14:20 or (resid...B1 - 264

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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: 29251.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS A N775S-MUTANT OF THE GLUA2 LIGAND-BINDING DOMAIN. THE SEQUENCE MATCHES DISCONTINUOUSLY WITH REFERENCE DATABASE (413-527, 653- ...Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS A N775S-MUTANT OF THE GLUA2 LIGAND-BINDING DOMAIN. THE SEQUENCE MATCHES DISCONTINUOUSLY WITH REFERENCE DATABASE (413-527, 653-797). TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119) AND GLY1-ALA2 IS CLONING REMNANT.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

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Non-polymers , 8 types, 685 molecules

#2: Chemical ChemComp-FXW / 6,6'-(ETHANE-1,2-DIYL)BIS(4-CYCLOPROPYL-3,4-DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE)


Mass: 474.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N4O4S2
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 24% PEG4000, 0.3 M lithium sulfate, 0.1 M phosphate citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.617→29.74 Å / Num. all: 72996 / Num. obs: 72996 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 16.71 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.104 / Rsym value: 0.097 / Net I/av σ(I): 6.3 / Net I/σ(I): 11 / Num. measured all: 548555
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.62-1.77.50.6341.178565104540.2440.680.6342.298.9
1.7-1.817.50.471.57485699560.1820.5050.473.299.4
1.81-1.937.50.322.26965493410.1240.3430.324.899.1
1.93-2.097.40.2173.36484487160.0840.2330.2177.199
2.09-2.297.50.1514.66042980590.0580.1620.15110.199.5
2.29-2.567.70.1255.55696373810.0480.1340.12512.3100
2.56-2.957.60.0927.45017165830.0350.0990.09216.1100
2.95-3.627.50.05811.44181055910.0220.0620.05824.8100
3.62-5.117.60.04215.53331743690.0160.0450.04235.199.8
5.11-29.73870.04512.41794625460.0180.0480.0452899.5

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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: 1ftj

1ftj


Resolution: 1.617→29.738 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.54 / Phase error: 19.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 3627 4.97 %
Rwork0.1548 69279 -
obs0.1561 72906 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.44 Å2 / Biso mean: 25.7751 Å2 / Biso min: 8.85 Å2
Refinement stepCycle: final / Resolution: 1.617→29.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4096 0 279 681 5056
Biso mean--43.57 32.76 -
Num. residues----528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054497
X-RAY DIFFRACTIONf_angle_d0.8866088
X-RAY DIFFRACTIONf_chiral_restr0.049666
X-RAY DIFFRACTIONf_plane_restr0.005758
X-RAY DIFFRACTIONf_dihedral_angle_d16.1532775
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2422X-RAY DIFFRACTION3.063TORSIONAL
12B2422X-RAY DIFFRACTION3.063TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6172-1.63850.2641530.23332593274698
1.6385-1.6610.25751400.23452614275499
1.661-1.68470.23041410.20982603274499
1.6847-1.70980.26551320.2032620275299
1.7098-1.73650.21831380.19352613275199
1.7365-1.7650.20661430.1932625276899
1.765-1.79540.22641340.18772640277499
1.7954-1.82810.23481410.18632610275199
1.8281-1.86320.22141450.17552615276099
1.8632-1.90130.22781260.17782654278099
1.9013-1.94260.18941250.1772642276799
1.9426-1.98780.21351310.17622645277699
1.9878-2.03750.19771260.162647277399
2.0375-2.09260.19771510.15172605275699
2.0926-2.15410.1711450.1462647279299
2.1541-2.22360.16261190.143526602779100
2.2236-2.30310.16031470.134926622809100
2.3031-2.39520.16931370.135926852822100
2.3952-2.50420.16771390.140126802819100
2.5042-2.63610.14941240.141227262850100
2.6361-2.80120.15041370.143426922829100
2.8012-3.01730.1861430.15127072850100
3.0173-3.32060.17661570.144727052862100
3.3206-3.80020.16541480.139127212869100
3.8002-4.78470.14311460.127727712917100
4.7847-29.74350.20981590.175428973056100
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)
10.7589-0.058-0.35610.8857-0.1061.55780.05670.02350.0923-0.07930.01820.0049-0.16120.0019-0.05360.09120.00950.00870.0719-0.00320.096523.5544182.9123-34.345
22.29010.777-0.11482.32130.57761.7309-0.02270.0424-0.08220.11010.01660.25190.1049-0.16740.00160.09320.00360.01060.09440.01010.144210.4174174.1904-17.5642
30.9792-0.2213-0.78290.61740.29241.19350.025-0.11050.04660.00570.0301-0.0718-0.06370.1445-0.05210.12290.0045-0.00940.1363-0.00270.148230.2395177.4276-25.0739
41.81470.3833-0.15782.626-0.5440.3256-0.01080.0815-0.1699-0.1227-0.0426-0.03730.1397-0.02470.04390.20590.02510.02930.1193-0.00910.136533.1177143.1829-33.2652
51.1088-0.75760.39313.1151-0.98281.7644-0.01180.0298-0.1162-0.16510.01470.18530.078-0.0587-0.00920.1884-0.01460.00790.111-0.00060.136527.3115142.8528-32.7648
64.8440.32321.00162.25130.45362.0327-0.00460.1818-0.2845-0.15350.0639-0.23930.2350.1951-0.04660.20780.04670.04550.12920.00910.088238.4666148.612-37.8755
72.2563-0.5846-0.14062.02830.70282.6157-0.12120.07690.0661-0.20560.1127-0.27990.1640.43470.0420.16850.03250.03970.17610.00410.132642.6486154.8379-39.8559
81.2519-0.05740.42850.9566-0.50431.8465-0.0031-0.15520.05040.0576-0.0637-0.0380.02620.08690.06370.11620.01940.01870.12430.00010.128239.3368161.4274-24.3021
92.73260.0914-0.3491.9861-0.37811.5990.0098-0.17740.03120.0884-0.2031-0.33970.03940.45660.15160.130.02410.00450.24130.04840.182249.1334158.817-18.5196
100.1543-0.30520.27495.2113-3.00272.8857-0.0516-0.1404-0.11840.3442-0.08380.27060.09040.00790.13920.22540.01350.06420.2460.00270.219538.8301156.7355-12.3493
111.6134-0.4445-0.49361.3020.44272.01420.01940.190.0363-0.1803-0.01160.01820.0376-0.0065-0.00230.14930.00880.00550.10810.01030.122526.699159.2634-37.8822
121.23280.0380.48941.8846-1.07294.3885-0.036-0.4961-0.110.57130.05140.07480.2426-0.1811-0.06470.35750.00010.04030.19120.02030.168925.3438150.499-17.3415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 116 )A1 - 116
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 202 )A117 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 263 )A203 - 263
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 22 )B1 - 22
5X-RAY DIFFRACTION5chain 'B' and (resid 23 through 47 )B23 - 47
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 65 )B48 - 65
7X-RAY DIFFRACTION7chain 'B' and (resid 66 through 93 )B66 - 93
8X-RAY DIFFRACTION8chain 'B' and (resid 94 through 123 )B94 - 123
9X-RAY DIFFRACTION9chain 'B' and (resid 124 through 202 )B124 - 202
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 217 )B203 - 217
11X-RAY DIFFRACTION11chain 'B' and (resid 218 through 244 )B218 - 244
12X-RAY DIFFRACTION12chain 'B' and (resid 245 through 263 )B245 - 263

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