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- PDB-6giv: Structure of GluA2-N775S ligand-binding domain (S1S2J) in complex... -

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Basic information

Entry
Database: PDB / ID: 6giv
TitleStructure of GluA2-N775S ligand-binding domain (S1S2J) in complex with glutamate and Rubidium Bromide at 1.75 A resolution
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / Ionotropic glutamate receptor / GluA2-N775S ligand-binding domain / agonist / bromide ions
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor 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 / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor 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 signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / 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 / endoplasmic reticulum membrane / 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
BROMIDE ION / GLUTAMIC ACID / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsVenskutonyte, R. / Frydenvang, K. / Kastrup, J.S.
CitationJournal: Neuron / Year: 2019
Title: Nanoscale Mobility of the Apo State and TARP Stoichiometry Dictate the Gating Behavior of Alternatively Spliced AMPA Receptors.
Authors: Dawe, G.B. / Kadir, M.F. / Venskutonyte, R. / Perozzo, A.M. / Yan, Y. / Alexander, R.P.D. / Navarrete, C. / Santander, E.A. / Arsenault, M. / Fuentes, C. / Aurousseau, M.R.P. / Frydenvang, K. ...Authors: Dawe, G.B. / Kadir, M.F. / Venskutonyte, R. / Perozzo, A.M. / Yan, Y. / Alexander, R.P.D. / Navarrete, C. / Santander, E.A. / Arsenault, M. / Fuentes, C. / Aurousseau, M.R.P. / Frydenvang, K. / Barrera, N.P. / Kastrup, J.S. / Edwardson, J.M. / Bowie, D.
History
DepositionMay 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8517
Polymers29,2521
Non-polymers5996
Water4,756264
1
A: Glutamate receptor 2
hetero molecules

A: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,70214
Polymers58,5032
Non-polymers1,19912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3690 Å2
ΔGint-39 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.956, 47.513, 49.810
Angle α, β, γ (deg.)90.000, 110.160, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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.: 1 / Mutation: N775S,N775S
Source method: isolated from a genetically manipulated source
Details: The protein crystallized is the extracellular ligand-binding domain of GluA2-N775S. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The ...Details: The protein crystallized is the extracellular ligand-binding domain of GluA2-N775S. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residue 118-119). The sequence matches discontinously with the reference database (UNP residues 413-527 and 653-797, numbering with signal peptide of 21 amino acids). The two first residues (GLY, ALA) are cloning remnants.
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 (DE3) / References: UniProt: P19491

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Non-polymers , 5 types, 270 molecules

#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18-24.4% PEG4000, 0.2-0.3 M Li2SO4, and 0.1 M cacodylate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91976 Å / Relative weight: 1
ReflectionResolution: 1.75→46.76 Å / Num. obs: 27430 / % possible obs: 100 % / Redundancy: 5 % / Biso Wilson estimate: 15.4 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.089 / Rsym value: 0.074 / Net I/av σ(I): 7.5 / Net I/σ(I): 11.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.75-1.844.70.3731.839980.2030.4510.373100
1.84-1.9650.262.637400.1360.3140.26100
1.96-2.095.10.1534.435530.0810.1850.153100
2.09-2.265.10.1195.332830.0620.1430.119100
2.26-2.475.10.097.730470.0470.1090.09100
2.47-2.775.10.0719.327700.0360.0850.071100
2.77-3.25.10.05910.524190.030.070.059100
3.2-3.915.10.05311.920820.0260.0620.053100
3.91-5.5350.04413.916260.0210.0510.044100
5.53-46.764.80.0414.99120.020.0470.0499.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.75 Å43.94 Å
Translation1.75 Å43.94 Å

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O3A

4o3a


Resolution: 1.75→34.346 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.59
RfactorNum. reflection% reflection
Rfree0.1904 1376 5.02 %
Rwork0.1561 --
obs0.1578 27411 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.1 Å2 / Biso mean: 23.9456 Å2 / Biso min: 9 Å2
Refinement stepCycle: final / Resolution: 1.75→34.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2037 0 34 267 2338
Biso mean--43.36 29.21 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052158
X-RAY DIFFRACTIONf_angle_d0.7522914
X-RAY DIFFRACTIONf_chiral_restr0.049324
X-RAY DIFFRACTIONf_plane_restr0.005363
X-RAY DIFFRACTIONf_dihedral_angle_d13.2491328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.81260.25191280.207526082736
1.8126-1.88510.22951520.18525472699
1.8851-1.97090.28341330.227626072740
1.9709-2.07480.21371310.16125892720
2.0748-2.20480.19361310.146625712702
2.2048-2.3750.22811340.180326162750
2.375-2.61390.17131300.155925962726
2.6139-2.9920.18591340.1526242758
2.992-3.76880.18111460.140626012747
3.7688-34.35270.14771570.131326762833
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)
12.10140.43340.35142.6785-0.11372.45520.02650.1432-0.1616-0.13370.01360.0292-0.0273-0.0291-0.02270.15070.0034-0.05220.1057-0.0090.1273-22.129412.28254.5892
23.8874-1.3092-2.12672.27791.54193.89920.01510.0886-0.06480.0621-0.02330.06450.1151-0.21130.09140.1008-0.0125-0.05190.0777-0.00070.1337-26.07517.501313.6771
36.7661-0.94971.37887.66661.5161.1661-0.0451-0.6132-0.25270.39860.03080.99620.1894-0.00370.06020.1356-0.00410.02170.12660.01690.2445-29.37394.233924.6411
40.3906-0.5879-0.33532.57880.16650.52860.0001-0.0141-0.01890.03190.0178-0.04380.01590.0242-0.0140.1014-0.0044-0.050.11230.01040.1235-20.156616.437222.6899
51.513-0.3654-0.13031.8517-0.69053.2612-0.0078-0.175-0.0790.08950.0840.1735-0.0803-0.1701-0.0730.10750.0033-0.0310.10970.02280.1303-29.164726.585828.4168
64.6537-3.80794.20545.907-4.95396.95680.08360.03760.0329-0.0308-0.0362-0.11690.09920.05790.01530.1522-0.0173-0.01770.11020.00240.1529-21.364732.168220.8283
72.65460.4018-0.85952.9599-0.94052.2655-0.1198-0.0278-0.2861-0.1370.0211-0.05550.16710.09040.10650.09450.0069-0.05450.1025-0.00540.1187-10.8367.113715.9855
85.0758-3.4922-1.35097.7588-0.2873.98160.15790.30220.4717-0.1039-0.1603-0.2991-0.327-0.1034-0.01930.1944-0.0373-0.05480.14750.04660.1407-13.165925.77888.0679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 65 )A48 - 65
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 79 )A66 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 123 )A80 - 123
5X-RAY DIFFRACTION5chain 'A' and (resid 124 through 202 )A124 - 202
6X-RAY DIFFRACTION6chain 'A' and (resid 203 through 217 )A203 - 217
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 243 )A218 - 243
8X-RAY DIFFRACTION8chain 'A' and (resid 244 through 262 )A244 - 262

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