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

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Basic information

Entry
Database: PDB / ID: 6hcb
TitleSTRUCTURE OF GLUA2 LIGAND-BINDING DOMAIN (S1S2J-N775S) IN COMPLEX WITH GLUTAMATE AND TDPAM01 AT 1.9 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 / 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-D45 / GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLaulumaa, S. / Masternak, M. / 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 1.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.2Jan 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

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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)60,80724
Polymers58,5032
Non-polymers2,30422
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-154 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.436, 122.025, 47.623
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 (resid 4 through 21 or resid 23...
21(chain B and (resid 4 through 21 or resid 23...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 21 or resid 23...A4 - 21
121(chain A and (resid 4 through 21 or resid 23...A23 - 53
131(chain A and (resid 4 through 21 or resid 23...A4 - 262
141(chain A and (resid 4 through 21 or resid 23...A4 - 262
151(chain A and (resid 4 through 21 or resid 23...A165
161(chain A and (resid 4 through 21 or resid 23...A1 - 195
171(chain A and (resid 4 through 21 or resid 23...A210 - 216
181(chain A and (resid 4 through 21 or resid 23...A4 - 262
191(chain A and (resid 4 through 21 or resid 23...A218 - 262
211(chain B and (resid 4 through 21 or resid 23...B4 - 21
221(chain B and (resid 4 through 21 or resid 23...B23 - 53
231(chain B and (resid 4 through 21 or resid 23...B1 - 262
241(chain B and (resid 4 through 21 or resid 23...B1 - 262
251(chain B and (resid 4 through 21 or resid 23...B165
261(chain B and (resid 4 through 21 or resid 23...B1 - 195
271(chain B and (resid 4 through 21 or resid 23...B210 - 216
281(chain B and (resid 4 through 21 or resid 23...B1 - 262
291(chain B and (resid 4 through 21 or resid 23...B218 - 262

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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.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 , 7 types, 324 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#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-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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-D45 / 6,6'-(Ethane-1,2-diyl)bis(4-methyl-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide)


Mass: 422.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N4O4S2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 48.96 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 15% PEG4000, 0.1 M ammonium sulphate, 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 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→48.72 Å / Num. obs: 45663 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 25.15 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.136 / Rsym value: 0.131 / Net I/av σ(I): 3.5 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.9-212.50.66165510.1940.6890.66100
2-2.1212.40.4571.362010.1340.4760.457100
2.12-2.2713.60.321.959010.090.3330.32100
2.27-2.4513.90.2472.354270.0680.2560.247100
2.45-2.6913.80.2012.750650.0560.2090.201100
2.69-313.70.1653.345980.0460.1710.165100
3-3.4713.50.1284.140780.0360.1330.128100
3.47-4.2513.60.0945.734810.0260.0980.094100
4.25-6.0113.70.0767.227530.0210.0790.076100
6.01-48.718120.0578.816080.0180.060.05799.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5o9a

5o9a


Resolution: 1.9→48.718 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.52 / Phase error: 20.12
RfactorNum. reflection% reflection
Rfree0.1918 2300 5.05 %
Rwork0.1691 --
obs0.1703 45505 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 126.88 Å2 / Biso mean: 35.5328 Å2 / Biso min: 13.93 Å2
Refinement stepCycle: final / Resolution: 1.9→48.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 222 302 4581
Biso mean--59.09 35.68 -
Num. residues----521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054315
X-RAY DIFFRACTIONf_angle_d0.7565818
X-RAY DIFFRACTIONf_chiral_restr0.049630
X-RAY DIFFRACTIONf_plane_restr0.004716
X-RAY DIFFRACTIONf_dihedral_angle_d15.7332615
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2959X-RAY DIFFRACTION5.079TORSIONAL
12B2959X-RAY DIFFRACTION5.079TORSIONAL
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 (%)
1.9-1.94130.26731300.22322637276799
1.9413-1.98650.23421310.214826842815100
1.9865-2.03620.22611520.194726342786100
2.0362-2.09120.22831330.179426502783100
2.0912-2.15280.20321310.169926882819100
2.1528-2.22220.20371440.17326622806100
2.2222-2.30170.20211320.171726902822100
2.3017-2.39380.19881610.16626632824100
2.3938-2.50280.17361450.176726862831100
2.5028-2.63470.19831480.172526672815100
2.6347-2.79980.17831440.178527202864100
2.7998-3.01590.22781460.186426792825100
3.0159-3.31940.19391490.168627162865100
3.3194-3.79950.1761260.159127642890100
3.7995-4.78630.14161630.131227712934100
4.7863-48.7340.21361650.180128943059100
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)
14.1276-0.18760.76612.77470.76023.0243-0.04890.0287-0.1285-0.24530.00050.03170.2654-0.01220.05210.3243-0.01320.03610.13620.00290.128229.9048143.206115.2929
21.24020.34080.54011.3871-0.01652.9539-0.04190.0696-0.0286-0.2103-0.0298-0.10430.2840.32240.04240.19760.06340.04960.17570.02710.161740.204155.939614.2655
34.74320.53170.3762.8207-0.76822.5366-0.1203-0.20870.1320.059-0.2527-0.42980.02840.39630.31530.17340.04380.00350.24540.05510.233647.6076158.700329.7704
44.04370.4210.24073.3551-1.32825.19640.0007-0.06920.1580.00360.08270.38820.3649-0.204-0.1350.1765-0.00140.01940.0557-0.02310.207125.8862155.817518.0588
53.9340.30140.65462.92-0.45532.81640.1404-0.05390.324-0.201-0.0804-0.1508-0.43470.2093-0.07550.2497-0.0330.05620.1569-0.01330.188729.6316190.214614.4638
60.58370.0011-0.99181.0464-0.44243.80470.05990.0465-0.0017-0.13830.01450.0687-0.071-0.2671-0.08380.14830.0179-0.0080.17210.00480.190719.078177.569414.3696
74.02370.8675-0.13213.29540.35372.4122-0.0580.0756-0.2620.12270.04720.35990.0696-0.17740.00110.10570.00060.02770.13040.01470.202511.5404174.794129.6567
83.66050.0653-0.08263.29081.40636.9585-0.002-0.1517-0.03810.01560.0196-0.4854-0.26260.3457-0.04070.1389-0.0116-0.00240.09280.02490.258133.3166177.81318.1355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 47 )A4 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 123 )A48 - 123
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 217 )A124 - 217
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 262 )A218 - 262
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 47 )B1 - 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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