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- PDB-6hca: STRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S1J) IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 6hca
TitleSTRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S1J) IN COMPLEX WITH POSITIVE ALLOSTERIC MODULATOR TDPAM02 AT 1.8 A RESOLUTION
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / GluA2-S1S2J / AMPA receptor / Ligand-binding domain / positive allosteric modulator / signaling protein
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 / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor binding / 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 membrane / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / postsynaptic density membrane / modulation of chemical synaptic transmission / establishment of protein localization / 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 / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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 / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.882 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

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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)60,95627
Polymers58,5572
Non-polymers2,39925
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-160 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.010, 91.392, 98.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:10 or (resid 11 and (name...
21(chain B and (resseq 5:10 or (resid 11 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
11THRTHRTHRTHR(chain A and (resseq 5:10 or (resid 11 and (name...AA5 - 105 - 10
12ILEILEILEILE(chain A and (resseq 5:10 or (resid 11 and (name...AA1111
13LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
14LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
15LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
16LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
17LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
18LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
19LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
110LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
111LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
112LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
113LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
114LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
115LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
116LYSLYSGLYGLY(chain A and (resseq 5:10 or (resid 11 and (name...AA4 - 2644 - 264
21THRTHRTHRTHR(chain B and (resseq 5:10 or (resid 11 and (name...BB5 - 105 - 10
22ILEILEILEILE(chain B and (resseq 5:10 or (resid 11 and (name...BB1111
23LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
24LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
25LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
26LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
27LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
28LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
29LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
210LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
211LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
212LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
213LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
214LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
215LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262
216LYSLYSGLYGLY(chain B and (resseq 5:10 or (resid 11 and (name...BB4 - 2624 - 262

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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: 29278.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS THE LIGAND-BINDING DOMAIN OF GLUA2. TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119) AND GLY1-ALA2 ...Details: NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS THE LIGAND-BINDING DOMAIN OF GLUA2. TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119) AND GLY1-ALA2 IS A CLONING REMNANT. THE SEQUENCE MATCHES DISCONTINUOUSLY WITH REFERENCE DATABASE (413-527, 653-797).,NATIVE GLUA2 IS A MEMBRANE PROTEIN. THE CRYSTALLIZED PROTEIN IS THE LIGAND-BINDING DOMAIN OF GLUA2. TRANSMEMBRANE REGIONS ARE REPLACED WITH A GLY-THR LINKER (RESIDUES 118-119) AND GLY1-ALA2 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: PET22B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ORIGAMI B / References: UniProt: P19491

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Non-polymers , 6 types, 568 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: 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
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
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: 1.882→29.58 Å / Num. all: 46079 / Num. obs: 46079 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 23.63 Å2 / Rpim(I) all: 0.042 / Rrim(I) all: 0.116 / Rsym value: 0.108 / Net I/av σ(I): 5.9 / Net I/σ(I): 10.7 / Num. measured all: 343924
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
1.88-1.987.40.71814849665280.2780.7710.7182.498.4
1.98-2.17.60.491.54795862980.1880.5250.493.6100
2.1-2.257.50.3392.24459059370.1310.3640.3395.1100
2.25-2.437.50.2534122155270.0970.2690.256.6100
2.43-2.667.40.1794.13781851210.070.1930.1798.7100
2.66-2.987.30.1265.63416846540.0490.1350.12611.8100
2.98-3.447.70.0828.13163941290.0320.0880.08218.7100
3.44-4.217.50.05910.82625335020.0230.0640.05925.9100
4.21-5.957.40.04812.92042727670.0190.0510.04827.6100
5.95-29.57770.03616.61135416160.0140.0390.03626.199.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1fto

1fto


Resolution: 1.882→29.577 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.76 / Phase error: 20.61
RfactorNum. reflection% reflection
Rfree0.2075 2270 4.94 %
Rwork0.171 --
obs0.1728 45991 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.54 Å2 / Biso mean: 32.7696 Å2 / Biso min: 13.61 Å2
Refinement stepCycle: final / Resolution: 1.882→29.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4055 0 229 547 4831
Biso mean--50.67 35.22 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074296
X-RAY DIFFRACTIONf_angle_d0.8835793
X-RAY DIFFRACTIONf_chiral_restr0.051627
X-RAY DIFFRACTIONf_plane_restr0.005708
X-RAY DIFFRACTIONf_dihedral_angle_d15.3492590
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2696X-RAY DIFFRACTION4.095TORSIONAL
12B2696X-RAY DIFFRACTION4.095TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8823-1.92330.26531400.24282594273496
1.9233-1.9680.26541480.225526782826100
1.968-2.01720.25061220.205527172839100
2.0172-2.07170.21671480.186127112859100
2.0717-2.13270.22691380.187427052843100
2.1327-2.20150.26641310.173127202851100
2.2015-2.28010.21171350.169527272862100
2.2801-2.37140.22111520.165426872839100
2.3714-2.47930.22951440.170627302874100
2.4793-2.60990.21371290.161227442873100
2.6099-2.77330.19311450.170727222867100
2.7733-2.98730.23941320.177827542886100
2.9873-3.28750.20561360.1727642900100
3.2875-3.76240.17771380.156427722910100
3.7624-4.73710.171630.140227772940100
4.7371-29.58080.20841690.185529193088100
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)
12.59180.7581-0.20742.4103-0.19042.00060.0252-0.1554-0.66980.032-0.0828-0.09470.3207-0.10770.02140.2076-0.04070.00790.16120.03760.309164.06227.599747.0898
21.25210.08371.12021.04190.01623.621-0.0058-0.052-0.06720.041-0.01150.0040.0142-0.2563-0.01610.1363-0.02630.01930.15140.00980.15963.28543.520544.6061
33.0597-0.24240.80133.07060.46641.5751-0.1120.1020.1353-0.04430.0310.0417-0.05640.0140.07960.2129-0.0316-0.00060.2074-0.00160.147257.711749.118628.1076
42.6017-0.021.66571.76960.79983.16320.06230.163-0.3206-0.08870.1209-0.23250.20640.0745-0.18690.1898-0.02840.03380.1530.01190.267374.355734.744741.4263
54.5171.67570.12374.02440.71892.6253-0.05350.01650.5386-0.0829-0.02210.0175-0.33560.09450.04970.2059-0.0067-0.04830.15480.03430.201887.233966.957346.0765
61.27950.106-0.70620.73640.08782.48580.0322-0.1319-0.08980.0648-0.0729-0.11970.02780.13320.02320.1591-0.0113-0.020.15890.02450.188989.776151.008946.0237
72.8959-0.1585-0.55413.6034-0.57971.488-0.02640.0072-0.34350.0328-0.0305-0.07720.04820.11460.05690.2244-0.0244-0.00160.2337-0.02370.177194.018244.640727.3655
82.5616-0.3997-0.82371.9575-0.12522.66480.08980.03730.2038-0.09480.0150.0993-0.1215-0.0554-0.1050.1519-0.0266-0.01530.14430.00620.169477.779957.752642.9468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 65 )A4 - 65
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 123 )A66 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 217 )A124 - 217
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 264 )A218 - 264
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 47 )B4 - 47
6X-RAY DIFFRACTION6chain 'B' and (resid 48 through 123 )B48 - 123
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 217 )B124 - 217
8X-RAY DIFFRACTION8chain 'B' and (resid 218 through 262 )B218 - 262

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