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- PDB-3h5w: Crystal structure of the GluR2-ATD in space group P212121 without... -

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Basic information

Entry
Database: PDB / ID: 3h5w
TitleCrystal structure of the GluR2-ATD in space group P212121 without solvent
ComponentsGlutamate receptor 2
KeywordsTRANSPORT PROTEIN / Glutamate receptor / Ligand-gated ion channel / synapse / Alternative splicing / Cell junction / Cell membrane / Endoplasmic reticulum / Glycoprotein / Ion transport / Ionic channel / Lipoprotein / Membrane / Palmitate / Phosphoprotein / Postsynaptic cell membrane / Receptor / RNA editing / Transmembrane / Transport
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 / immunoglobulin binding ...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 / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / 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 / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / ionotropic glutamate receptor binding / extracellular ligand-gated monoatomic ion channel activity / presynaptic active zone membrane / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / dendrite membrane / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / 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
Response regulator / 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 ...Response regulator / 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 I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.686 Å
AuthorsJin, R. / Singh, S.K. / Gu, S. / Furukawa, H. / Sobolevsky, A. / Zhou, J. / Jin, Y. / Gouaux, E.
CitationJournal: Embo J. / Year: 2009
Title: Crystal structure and association behaviour of the GluR2 amino-terminal domain.
Authors: Jin, R. / Singh, S.K. / Gu, S. / Furukawa, H. / Sobolevsky, A.I. / Zhou, J. / Jin, Y. / Gouaux, E.
History
DepositionApr 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 2
B: Glutamate receptor 2


Theoretical massNumber of molelcules
Total (without water)89,0192
Polymers89,0192
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-13 kcal/mol
Surface area31950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.866, 96.358, 108.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate receptor 2 / GluR-2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / AMPA-selective glutamate receptor 2


Mass: 44509.250 Da / Num. of mol.: 2 / Fragment: UNP residues 21-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P19491
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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG3000, 100mM tri-sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 24737 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.9
Reflection shellResolution: 2.68→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3H5V

3h5v


Resolution: 2.686→19.96 Å / SU ML: 0.46 / σ(F): 1.34 / Phase error: 29.67 / Stereochemistry target values: ML
Details: A HIGHER RESOLUTION STRUCTURE OF THE SAME PROTEIN IN A DIFFERENT CRYSTAL FORM HAS BEEN DEPOSITED IN PDB AS 3H5V. THE CONFORMATION OF THE PROTOMERS IN 3H5W IS SIMILAR TO THAT OF THE PROTOMERS ...Details: A HIGHER RESOLUTION STRUCTURE OF THE SAME PROTEIN IN A DIFFERENT CRYSTAL FORM HAS BEEN DEPOSITED IN PDB AS 3H5V. THE CONFORMATION OF THE PROTOMERS IN 3H5W IS SIMILAR TO THAT OF THE PROTOMERS IN THE HIGHER RESOLUTION, WELL REFINED 3H5V, AND THUS FURTHER REFINEMENT OF THIS CRYSTAL FORM WAS NOT PURSUED
RfactorNum. reflection% reflection
Rfree0.2908 1292 5.1 %
Rwork0.2153 --
obs0.2191 24737 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.423 Å2 / ksol: 0.302 e/Å3
Refinement stepCycle: LAST / Resolution: 2.686→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5404 0 0 0 5404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085513
X-RAY DIFFRACTIONf_angle_d1.0997490
X-RAY DIFFRACTIONf_dihedral_angle_d16.7691835
X-RAY DIFFRACTIONf_chiral_restr0.071843
X-RAY DIFFRACTIONf_plane_restr0.004984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.686-2.79280.34991300.25672381X-RAY DIFFRACTION90
2.7928-2.91950.35131480.25162676X-RAY DIFFRACTION100
2.9195-3.07290.34171410.25752688X-RAY DIFFRACTION100
3.0729-3.26470.38461410.24642640X-RAY DIFFRACTION100
3.2647-3.51550.33511430.23822693X-RAY DIFFRACTION100
3.5155-3.86690.28031490.20192693X-RAY DIFFRACTION100
3.8669-4.42120.23361610.182697X-RAY DIFFRACTION100
4.4212-5.55030.28661510.18792708X-RAY DIFFRACTION99
5.5503-19.96070.25681280.21042848X-RAY DIFFRACTION99
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)
11.5605-1.63470.42165.70641.58265.0611-0.09890.1847-0.0065-0.0754-0.16410.2760.3467-0.29910.23340.29870.00610.1070.3863-0.02440.2862-1.68353.95335.5706
23.47950.1348-0.89884.74460.71011.92940.19750.314-0.15170.8011-0.4053-0.3101-0.05740.17640.2420.2171-0.0601-0.1450.23690.13280.535417.610120.948121.3326
38.16172.00544.2975.80611.82465.8036-1.3499-1.68120.6247-0.7424-1.35970.4683-1.3533-0.63941.51311.2667-0.0142-0.38071.11040.35870.961316.836512.793838.6569
42.5405-0.9167-0.4986-3.13161.90280.7971-0.2393-0.0266-0.57690.77170.39650.6080.0251-0.3557-0.12920.8151-0.0126-0.06030.29480.19720.45417.613720.549631.7289
52.9537-1.3983-0.42996.0226-5.91413.0357-0.1738-1.04830.95142.06340.4121-0.044-1.8307-0.3656-0.32930.99560.02730.20010.4490.0030.55010.38822.804233.3215
61.0146-0.2920.7482.65291.45773.4679-0.0947-0.31950.1275-0.1476-0.35360.4296-0.4496-1.1440.42010.38590.1890.04930.5821-0.12850.4376-9.549818.974512.952
73.1382-4.0806-1.57465.94030.3792.23720.16511.15970.08161.109-0.7757-0.64410.2118-0.76210.28560.89190.3848-0.1921.1462-0.240.5992-1.10721.1214-10.1942
82.57570.5418-0.0382-1.0244-0.8021.17410.1640.45810.64080.10050.00120.1221-0.7317-0.0748-0.13750.55040.0670.03660.30590.16420.44713.943724.59957.8977
92.0374-0.0691.56281.8518-2.6730.8587-0.15340.43310.0328-0.7185-0.3186-0.17280.97820.43080.390.93790.38360.33520.62930.06660.430320.3411-15.392811.2824
10-2.5849-1.7138-0.33391.02840.36413.8939-0.6960.5280.58060.3049-0.40510.2788-0.01230.99790.9920.16910.0204-0.06580.73640.4040.947730.90428.22725.997
111.5019-2.56170.88035.6393-2.15140.72630.04290.90040.05010.1484-0.0621.0058-0.68510.1514-0.19231.67920.20170.0090.87870.28251.245635.58819.59611.7977
126.43838.5591.37153.84232.71192.40050.4101-1.05-0.9647-0.1404-1.8395-2.8774-1.3694-0.30880.90250.6980.10280.15190.87510.52450.893238.055613.85222.132
137.01826.67173.89786.57931.8972-3.4767-0.99450.5413-0.3686-1.05830.63990.36540.06831.11820.33831.8660.46780.00032.1052-0.01240.993942.303711.856511.1257
140.11280.60560.1725-1.3882-0.07320.49170.0302-0.2122-0.8942-1.2771-0.23-0.9260.44991.09660.1730.14410.41150.4091.30990.62510.990243.4420.342219.5719
15-0.34211.76040.4852.7848-0.72560.46810.31210.2656-0.4039-0.9921-0.5713-0.43251.35410.72950.3541.04570.77050.37450.9070.12750.555830.0447-21.736414.0589
16-0.23710.7164-0.77561.57190.17951.05780.0096-0.4307-0.0313-0.4791-0.578-0.25090.72990.61210.53520.64230.39120.28380.7920.38240.562929.13-13.016726.625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:108)A4 - 108
2X-RAY DIFFRACTION2(CHAIN A AND RESID 109:159)A109 - 159
3X-RAY DIFFRACTION3(CHAIN A AND RESID 160:182)A160 - 182
4X-RAY DIFFRACTION4(CHAIN A AND RESID 183:225)A183 - 225
5X-RAY DIFFRACTION5(CHAIN A AND RESID 226:234)A226 - 234
6X-RAY DIFFRACTION6(CHAIN A AND RESID 235:290)A235 - 290
7X-RAY DIFFRACTION7(CHAIN A AND RESID 291:319)A291 - 319
8X-RAY DIFFRACTION8(CHAIN A AND RESID 320:378)A320 - 378
9X-RAY DIFFRACTION9(CHAIN B AND RESID 6:108)B6 - 108
10X-RAY DIFFRACTION10(CHAIN B AND RESID 109:159)B109 - 159
11X-RAY DIFFRACTION11(CHAIN B AND RESID 160:180)B160 - 180
12X-RAY DIFFRACTION12(CHAIN B AND RESID 181:189)B181 - 189
13X-RAY DIFFRACTION13(CHAIN B AND RESID 190:209)B190 - 209
14X-RAY DIFFRACTION14(CHAIN B AND RESID 210:246)B210 - 246
15X-RAY DIFFRACTION15(CHAIN B AND RESID 247:311)B247 - 311
16X-RAY DIFFRACTION16(CHAIN B AND RESID 312:377)B312 - 377

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