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- PDB-6hc9: STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504Y-N775S) IN C... -

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Basic information

Entry
Database: PDB / ID: 6hc9
TitleSTRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-L504Y-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM02 AT 2.4 A RESOLUTION.
ComponentsGlutamate receptor 2,
KeywordsMEMBRANE PROTEIN / ampa receptor / gluA2 / ligand-binding domain / glua2-S1S2J-L504Y-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 / 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-FXW / GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / struct_ncs_dom_lim
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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 9, 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)60,95025
Polymers58,6032
Non-polymers2,34623
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-153 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.656, 121.942, 47.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:15 or (resid 16 and (name...
21(chain B and (resseq 5:15 or (resid 16 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRPROPRO(chain A and (resseq 5:15 or (resid 16 and (name...AA5 - 155 - 15
12TYRTYRTYRTYR(chain A and (resseq 5:15 or (resid 16 and (name...AA1616
13GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
14GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
15GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
16GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
17GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
18GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
19GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
110GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
111GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
112GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
113GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
114GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
115GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
116GLYGLYGLYGLY(chain A and (resseq 5:15 or (resid 16 and (name...AA1 - 2641 - 264
21THRTHRPROPRO(chain B and (resseq 5:15 or (resid 16 and (name...BB5 - 155 - 15
22TYRTYRTYRTYR(chain B and (resseq 5:15 or (resid 16 and (name...BB1616
23LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
24LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
25LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
26LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
27LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
28LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
29LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
210LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
211LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
212LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
213LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
214LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
215LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
216LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261
217LYSLYSCYSCYS(chain B and (resseq 5:15 or (resid 16 and (name...BB4 - 2614 - 261

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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: 29301.729 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 L540Y- N775S-MUTANT OF THE GLUA2 LIGAND-BINDING DOMAIN. TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES ...Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS A L540Y- N775S-MUTANT OF THE GLUA2 LIGAND-BINDING DOMAIN. TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119) AND GLY1 IS A CLONING REMNANT. THE SEQUENCE MATCHES DISCONTINUOUSLY WITH REFERENCE DATABASE (413-527, 653-797).
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, 235 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


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


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: 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 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 48.96 %
Crystal growTemperature: 291 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
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.981 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.4→121.94 Å / Num. all: 22932 / Num. obs: 22932 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 28.14 Å2 / Rpim(I) all: 0.107 / Rrim(I) all: 0.295 / Rsym value: 0.275 / Net I/av σ(I): 2.3 / Net I/σ(I): 4.9 / Num. measured all: 172168
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.4-2.537.40.9160.832670.3590.9850.916100
2.53-2.687.50.719131020.2810.7730.719100
2.68-2.877.80.5741.329450.2190.6150.574100
2.87-3.17.70.4381.627450.1680.4690.438100
3.1-3.397.60.32.425480.1150.3220.3100
3.39-3.797.60.219322800.0840.2350.219100
3.79-4.387.40.173.620660.0660.1820.17100
4.38-5.377.50.1523.917570.0580.1630.152100
5.37-7.597.40.1623.813880.0630.1750.162100
7.59-76.2256.30.1174.28340.050.1280.11799.8

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTJ

1ftj


Resolution: 2.4→76.225 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.13
RfactorNum. reflection% reflection
Rfree0.2391 1123 4.91 %
Rwork0.2081 --
obs0.2097 22873 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.15 Å2 / Biso mean: 34.0179 Å2 / Biso min: 0.78 Å2
Refinement stepCycle: final / Resolution: 2.4→76.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4072 0 227 214 4513
Biso mean--48.13 26.46 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024285
X-RAY DIFFRACTIONf_angle_d0.5765764
X-RAY DIFFRACTIONf_chiral_restr0.041621
X-RAY DIFFRACTIONf_plane_restr0.002708
X-RAY DIFFRACTIONf_dihedral_angle_d17.1252578
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2714X-RAY DIFFRACTION7.308TORSIONAL
12B2714X-RAY DIFFRACTION7.308TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.50920.33671410.271426632804
2.5092-2.64150.26631280.252626932821
2.6415-2.8070.26221320.233826642796
2.807-3.02380.26341260.233727002826
3.0238-3.32810.28051560.21826762832
3.3281-3.80970.21471380.195627222860
3.8097-4.79970.20011590.159127492908
4.7997-76.26370.2211430.20728833026
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)
11.163-0.034-0.47640.5439-0.50512.26350.11290.01940.2133-0.11330.0030.019-0.21670.0164-0.10310.2250.0040.03220.18710.00480.260822.9125182.1565-32.6011
22.26390.80110.27152.35810.15051.4517-0.01340.1154-0.0880.0762-0.00640.27430.0852-0.21660.01360.210.00570.00850.24790.01240.25329.7592174.248-18.5312
30.99620.0508-0.92480.8620.60041.6518-0.0116-0.17160.05210.03740.0553-0.1724-0.20370.248-0.05640.22710.0226-0.0370.276-0.0160.327430.1358177.2026-25.5766
41.83250.210.22911.62790.35271.52290.0649-0.1095-0.2835-0.00730.02510.15050.2828-0.137-0.08990.3984-0.00850.04160.20770.01410.279629.9729143.0847-32.2511
52.48-0.35580.15052.0667-0.34071.7029-0.15860.1764-0.2641-0.41720.0356-0.25850.13350.25120.1650.35460.01750.01710.2902-0.04490.252438.4053148.6351-37.8604
61.55410.1105-0.13041.21480.43411.84430.09870.06290.102-0.0941-0.0231-0.18670.03270.2385-0.0740.26240.01780.0270.2591-0.0020.265940.2303158.0882-34.9876
72.45480.0443-0.17333.254-1.01592.7852-0.243-0.41440.1460.5122-0.1506-0.2429-0.37730.28290.38290.46-0.151-0.02710.72430.02760.421850.2765163.7908-8.4151
82.27610.4788-0.19351.6133-0.15131.6990.14450.17770.0535-0.1366-0.293-0.4151-0.00240.55180.14510.28630.05790.00280.42970.04660.439252.5484161.8899-23.3308
91.53460.8923-0.73611.9938-1.05521.871-0.0257-0.5047-0.36510.3821-0.133-0.19680.22590.19420.15840.39210.02740.01930.49050.04460.3742.2255153.7628-14.3092
101.6984-0.3171-0.21851.2970.03911.43530.05150.05390.046-0.29750.13670.18480.1637-0.0262-0.18810.29590.0325-0.00660.19930.01720.241827.114159.4829-37.9799
114.26030.55751.19073.7679-0.32383.8298-0.2404-0.3515-0.19520.4319-0.0387-0.55990.4181-0.63010.1840.4522-0.01220.08080.295-0.02160.283524.359151.3294-20.2349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 123 )A4 - 123
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 202 )A124 - 202
3X-RAY DIFFRACTION3chain 'A' and (resid 203 through 260 )A203 - 260
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 47 )B4 - 47
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 65 )B48 - 65
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 116 )B66 - 116
7X-RAY DIFFRACTION7chain 'B' and (resid 117 through 133 )B117 - 133
8X-RAY DIFFRACTION8chain 'B' and (resid 134 through 173 )B134 - 173
9X-RAY DIFFRACTION9chain 'B' and (resid 174 through 217 )B174 - 217
10X-RAY DIFFRACTION10chain 'B' and (resid 218 through 243 )B218 - 243
11X-RAY DIFFRACTION11chain 'B' and (resid 244 through 260 )B244 - 260

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