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- PDB-4o3b: Crystal structure of an open/closed glua2 ligand-binding domain d... -

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Basic information

Entry
Database: PDB / ID: 4o3b
TitleCrystal structure of an open/closed glua2 ligand-binding domain dimer at 1.91 A resolution
ComponentsGlutamate receptor 2
Keywordsmembrane protein/agonist / AMPA RECEPTOR LIGAND-BINDING DOMAIN / GLUA2 / membrane protein-agonist complex
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / perisynaptic space / Activation of AMPA receptors / ligand-gated monoatomic cation channel activity / AMPA glutamate receptor activity / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / kainate selective glutamate receptor activity / AMPA glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / asymmetric synapse / ionotropic glutamate receptor complex / conditioned place preference / regulation of receptor recycling / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / extracellular ligand-gated monoatomic ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / somatodendritic compartment / dendrite membrane / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / synaptic membrane / dendritic shaft / SNARE binding / 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 / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / receptor internalization / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / synaptic vesicle membrane / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / perikaryon / chemical synaptic transmission / dendritic spine / postsynaptic membrane / neuron projection / postsynaptic density / axon / external side of plasma membrane / neuronal cell body / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / 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
ACETATE ION / GLUTAMIC ACID / DI(HYDROXYETHYL)ETHER / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.906 Å
AuthorsKrintel, C. / de Rabassa, A.C. / Frydenvang, K. / Gajhede, M. / Kastrup, J.S.
Citation
Journal: Febs J. / Year: 2014
Title: L-Asp is a useful tool in the purification of the ionotropic glutamate receptor A2 ligand-binding domain.
Authors: Krintel, C. / Frydenvang, K. / Ceravalls de Rabassa, A. / Kaern, A.M. / Gajhede, M. / Pickering, D.S. / Kastrup, J.S.
#1: Journal: Neuron / Year: 2000
Title: Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core.
Authors: Armstrong, N. / Gouaux, E.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2May 31, 2017Group: Structure summary
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 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)59,92217
Polymers58,4432
Non-polymers1,47915
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-70 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.720, 93.720, 97.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 / AMPA 2


Mass: 29221.682 Da / Num. of mol.: 2
Fragment: Ligand binding domain (unp residues 413-527 and unp residues 653-736)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491

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Non-polymers , 8 types, 569 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 4000, 0.1 M lithium sulfate and 0.1 M phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.9081 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9081 Å / Relative weight: 1
ReflectionResolution: 1.91→27.96 Å / Num. all: 44501 / Num. obs: 45335 / % possible obs: 98.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.71 Å2 / Rsym value: 0.049 / Net I/σ(I): 19.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.91-2.013.30.0831154830.08392.1
2.01-2.133.80.07114.660520.071100
2.13-2.283.80.06216.957090.062100
2.28-2.463.80.05418.353180.05499.9
2.46-2.73.80.05220.848660.05299.9
2.7-3.013.80.0482343920.04899.9
3.01-3.483.80.04425.538670.04499.7
3.48-4.263.70.04328.532030.04399
4.26-6.033.60.04529.524110.04596.9
6.03-27.963.40.04228.512290.04287.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.91 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.5 Å
Translation2.5 Å27.5 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1FTL

1ftl


Resolution: 1.906→27.505 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.14 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.14 / Stereochemistry target values: ML
Details: Refinement done with TLS, isotropic B-factors and riding hydrogens
RfactorNum. reflection% reflectionSelection details
Rfree0.1782 2250 5.06 %RANDOM
Rwork0.1376 ---
obs0.1397 44448 97.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.59 Å2 / Biso mean: 20.881 Å2 / Biso min: 6.34 Å2
Refinement stepCycle: LAST / Resolution: 1.906→27.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4047 0 91 554 4692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114279
X-RAY DIFFRACTIONf_angle_d1.2515755
X-RAY DIFFRACTIONf_chiral_restr0.077633
X-RAY DIFFRACTIONf_plane_restr0.006713
X-RAY DIFFRACTIONf_dihedral_angle_d13.9951641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.9062-1.94770.22251170.160421692286216982
1.9477-1.9930.21311420.1397263527772635100
1.993-2.04280.20041450.1331266428092664100
2.0428-2.0980.17821440.1312266828122668100
2.098-2.15970.18351470.1266264227892642100
2.1597-2.22940.16981560.1241264127972641100
2.2294-2.3090.17951270.1241268028072680100
2.309-2.40140.15611380.1277268828262688100
2.4014-2.51070.1651330.133268128142681100
2.5107-2.64290.19671470.1352265928062659100
2.6429-2.80840.18321340.1385268828222688100
2.8084-3.0250.19361440.1427269328372693100
3.025-3.32890.1651480.1391269628442696100
3.3289-3.80950.1591420.133327092851270999
3.8095-4.79540.15011290.121626972826269797
4.7954-27.50780.21061570.186725882745258891
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)
14.40490.40960.56613.2419-0.25994.0310.00370.2144-0.0043-0.1527-0.0154-0.44040.21860.3253-0.03010.11090.010.02240.11460.01190.163140.782786.013226.9819
22.83331.1271-0.0864.321-0.25442.7147-0.0112-0.0294-0.16580.07960.093-0.06980.2070.0234-0.0330.05750.0317-0.01460.1063-0.00880.056530.480181.866736.5309
30.24560.24550.61250.86440.36173.3956-0.01280.0165-0.01410.04170.02710.01140.11120.0742-0.02060.05360.00380.01310.09230.00830.087122.239683.462426.6072
44.14760.56-2.13814.9996-0.49033.23850.0215-0.18980.01770.1204-0.07790.41060.1131-0.01680.06410.1158-0.0190.01260.104-0.02230.130714.800269.606514.9231
54.26252.92830.32736.72512.44134.0476-0.0981-0.1139-0.0264-0.3110.0378-0.1507-0.02770.4240.03820.1120.01120.01350.1470.03850.07425.051576.8899.8985
60.1767-0.20.21011.81261.37192.26290.04390.09030.0098-0.1928-0.0187-0.10120.00230.0977-0.01820.1166-0.01250.02350.11770.03160.102922.745783.330214.3909
71.4767-0.2328-1.10962.98590.37333.7880.01350.11320.1346-0.15160.0582-0.0193-0.15570.0493-0.0746-0-0.0191-0.02130.11360.00330.143728.429695.057824.5856
84.04380.3179-0.74332.9363-0.19882.4415-0.03420.1996-0.0107-0.02190.03760.2568-0.0935-0.31290.0130.0721-0.01190.0230.09640.00580.1312-5.7381100.627429.1231
97.8449-2.08731.60712.3803-0.50363.7349-0.0592-0.1234-0.26780.03150.11730.27720.0023-0.2209-0.03470.0926-0.03930.02760.09240.00570.1654-8.381695.180530.0263
102.86311.151-1.29895.8903-1.80242.135-0.0962-0.13980.016-0.00780.18130.46910.137-0.1758-0.10380.0910.01330.01610.12910.00940.0576-1.111398.951735.5725
112.21790.22450.9118.2758-0.04423.82070.0612-0.08030.10250.1038-0.1149-0.1968-0.70730.2260.03020.2038-0.02970.01980.1394-0.0220.07328.9442112.162338.5449
122.81430.8101-0.55573.1034-0.74113.80770.06250.00160.07130.0923-0.0407-0.1685-0.11810.1742-0.01350.06350.018-0.00430.0516-0.00830.078111.6265101.455534.6035
130.6737-0.350.83423.2901-3.62675.47140.06090.1179-0.0493-0.1846-0.0890.00830.06050.27430.06010.09120.01040.01380.0998-0.02190.070310.7883103.450212.9357
143.88410.5041-0.62884.4076-1.49475.5589-0.00630.29090.0683-0.2185-0.0557-0.105-0.28390.19530.02150.0634-0.0425-0.01250.081-0.0140.104514.7758114.494912.8293
157.4068-1.434-0.34564.7773-0.86921.9296-0.0037-0.3119-0.05530.3273-0.0694-0.5866-0.22340.31830.0280.12-0.0585-0.03530.1361-0.00130.156120.5226114.673519.4558
165.55623.8920.43435.92-0.34152.39160.005-0.06380.22180.12820.00540.2067-0.2691-0.0770.00410.06770.03380.01320.0754-0.01330.09994.8614117.416715.8687
172.54260.75460.62915.0349-2.03894.42670.00620.1032-0.1149-0.14570.15020.07930.1323-0.1881-0.12730.0580.00940.02160.1179-0.02280.05864.8996106.189212.4073
180.8265-0.6485-0.02221.4105-1.34612.06960.03450.06190.0315-0.1943-0.07880.07620.1579-0.08880.03610.1002-0.0088-0.00720.1031-0.04210.10888.8553101.685415.2017
191.59680.34880.40194.95655.94467.1129-0.0633-0.269-0.13090.4264-0.007-0.01960.29730.01460.03810.14540.01520.00670.12540.02540.13079.145589.72237.7657
203.0223-0.79161.96676.0356-4.76777.99080.12410.3406-0.1173-0.64530.03590.28040.4902-0.1171-0.14310.151-0.0255-0.03160.1498-0.06350.1778-0.082389.749717.0865
215.92694.23973.44923.14842.19572.64520.38170.771-0.1691-1.1299-0.0335-0.3076-0.462-0.3419-0.25020.19810.06390.02140.1535-0.0490.1259.1259106.25624.7763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:40 )A4 - 40
2X-RAY DIFFRACTION2( CHAIN A AND RESID 41:80 )A41 - 80
3X-RAY DIFFRACTION3( CHAIN A AND RESID 81:120 )A81 - 120
4X-RAY DIFFRACTION4( CHAIN A AND RESID 121:180 )A121 - 180
5X-RAY DIFFRACTION5( CHAIN A AND RESID 181:202 )A181 - 202
6X-RAY DIFFRACTION6( CHAIN A AND RESID 203:222 )A203 - 222
7X-RAY DIFFRACTION7( CHAIN A AND RESID 223:263 )A223 - 263
8X-RAY DIFFRACTION8( CHAIN B AND RESID 4:23 )B4 - 23
9X-RAY DIFFRACTION9( CHAIN B AND RESID 24:43 )B24 - 43
10X-RAY DIFFRACTION10( CHAIN B AND RESID 44:63 )B44 - 63
11X-RAY DIFFRACTION11( CHAIN B AND RESID 64:83 )B64 - 83
12X-RAY DIFFRACTION12( CHAIN B AND RESID 84:103 )B84 - 103
13X-RAY DIFFRACTION13( CHAIN B AND RESID 104:123 )B104 - 123
14X-RAY DIFFRACTION14( CHAIN B AND RESID 124:143 )B124 - 143
15X-RAY DIFFRACTION15( CHAIN B AND RESID 144:163 )B144 - 163
16X-RAY DIFFRACTION16( CHAIN B AND RESID 164:183 )B164 - 183
17X-RAY DIFFRACTION17( CHAIN B AND RESID 184:203 )B184 - 203
18X-RAY DIFFRACTION18( CHAIN B AND RESID 204:223 )B204 - 223
19X-RAY DIFFRACTION19( CHAIN B AND RESID 224:243 )B224 - 243
20X-RAY DIFFRACTION20( CHAIN B AND RESID 244:261 )B244 - 261
21X-RAY DIFFRACTION21( CHAIN B AND RESID 301:301 )B301

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