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- PDB-4h8j: Structure of GluA2-LBD in complex with MES -

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Basic information

Entry
Database: PDB / ID: 4h8j
TitleStructure of GluA2-LBD in complex with MES
ComponentsGlutamate receptor 2
KeywordsSIGNALING PROTEIN / membrane protein / glycoprotein / transmembrane protein / ligand-binding domain / ion transport / ion channel / ionotropic glutamate receptor / AMPA receptor / MES / synapse / postsynaptic cell membrane
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 / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / cytoskeletal protein binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor 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
Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsReiter, A. / Skerra, A. / Trauner, D. / Schiefner, A.
CitationJournal: To be Published
Title: Structural basis of an artificial photoreceptor
Authors: Reiter, A. / Volgraf, M. / Isacoff, E.Y. / Sumser, M. / Skerra, A. / Trauner, D. / Schiefner, A.
History
DepositionSep 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,45723
Polymers121,6044
Non-polymers1,85419
Water19,6181089
1
A: Glutamate receptor 2
B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,76012
Polymers60,8022
Non-polymers95810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-72 kcal/mol
Surface area25130 Å2
MethodPISA
2
C: Glutamate receptor 2
D: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,69811
Polymers60,8022
Non-polymers8969
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-76 kcal/mol
Surface area25120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.987, 92.020, 196.505
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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: 30400.891 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur2, Gria2 / Plasmid: pETGQ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19491
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1089 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPROTEIN COMPRISES RESIDUES 413-527 AND RESIDUES 653-797 OF UNP P19491 SEPARATED BY A GT LINKER.

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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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 23-27% w/v PEG3350, 0.2 M lithium sulfate, MES sodium, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 28, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 104956 / Num. obs: 104825 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 21.131 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.90.5213.89126729154871100
1.9-20.3575.78102665126361100
2-2.50.18510.73302159370341100
2.5-30.09918.61134554165181100
3-40.05330.5610409513223199.9
4-50.03837.04364304790199.9
5-60.04432.751632621441100
6-80.04333.761309817471100
8-100.03240.34506631199.7
10-200.03136.934150615185.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BFU

3bfu


Resolution: 1.8→19.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.1995 / WRfactor Rwork: 0.1564 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8519 / SU B: 4.858 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1226 / SU Rfree: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 5237 5 %RANDOM
Rwork0.1732 ---
obs0.1755 104824 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.61 Å2 / Biso mean: 16.213 Å2 / Biso min: 3.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8106 0 104 1089 9299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0228345
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.98511222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92651037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42524.321324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.276151575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2231540
X-RAY DIFFRACTIONr_chiral_restr0.120.21229
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216004
X-RAY DIFFRACTIONr_mcbond_it0.8491.55127
X-RAY DIFFRACTIONr_mcangle_it1.4832.58235
X-RAY DIFFRACTIONr_scbond_it3.0953.53218
X-RAY DIFFRACTIONr_scangle_it5.001102986
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 354 -
Rwork0.212 7227 -
all-7581 -
obs--99.99 %
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)
11.9279-0.5964-0.11652.21260.6541.71920.01250.11520.2583-0.103-0.08010.1129-0.1447-0.18110.06760.04760.0234-0.01040.05990.01730.06433.237112.7429-49.122
22.58960.0412-0.86292.72180.25161.5427-0.0754-0.0619-0.12680.0209-0.01790.04140.0728-0.01780.09330.04410.01440.00870.089300.0324-2.342-2.9519-27.7297
32.6574-0.0732-1.22751.5590.40582.16570.0448-0.12810.1460.06560.0563-0.1049-0.07020.075-0.1010.02880.0006-0.01590.0140.00410.061513.805511.3264-41.7012
41.013-0.60950.00012.2938-0.33981.1611-0.00470.1058-0.1455-0.0636-0.0431-0.07540.070.09980.04780.03320.0160.0020.0563-0.0160.044427.5779-11.9577-49.9828
52.4789-0.08550.65413.02090.01411.5402-0.0553-0.04680.1502-0.02480.02640.0093-0.06530.03830.02890.0550.0252-0.00810.1002-0.02750.023632.91980.9195-27.0131
62.41670.33370.67581.6915-0.43322.98680.0296-0.1119-0.15090.02420.00560.08790.1516-0.0653-0.03520.02730.00350.00390.0201-0.01480.062116.8041-11.3387-43.5934
71.6977-1.02470.33363.332-0.85031.70770.07380.17-0.258-0.2136-0.1265-0.10890.19280.20390.05270.06760.03560.00710.0737-0.02860.068530.003-12.3697-0.5109
82.89110.13241.05842.5543-0.03841.3346-0.0879-0.09350.12370.0422-0.0161-0.0038-0.095-0.02050.1040.05460.0242-0.00810.0757-0.00550.01935.58792.509821.4736
93.24760.14011.41481.9018-0.85922.62780.0666-0.1403-0.1915-0.01780.04970.20110.1353-0.0766-0.11630.03470.00610.00170.0248-0.01050.087619.4133-11.29836.9881
101.2908-0.71250.00442.29180.42871.2429-0.01740.0950.1267-0.0463-0.04220.1206-0.0797-0.12480.05970.03720.0049-0.01030.05350.01020.0355.767212.3955-0.363
112.8846-0.2129-0.59852.96860.15731.356-0.0488-0.0684-0.1893-0.02970.00750.00990.0209-0.00340.04130.05890.020.00280.09550.02460.01740.4605-1.365122.1135
122.80320.1132-0.74432.15210.31792.8793-0.0024-0.0610.1620.05140.0265-0.0684-0.14830.0623-0.02410.02020.0007-0.00860.00970.00950.047316.546111.58935.6602
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 108
2X-RAY DIFFRACTION2A109 - 217
3X-RAY DIFFRACTION3A218 - 264
4X-RAY DIFFRACTION4B4 - 109
5X-RAY DIFFRACTION5B110 - 216
6X-RAY DIFFRACTION6B217 - 262
7X-RAY DIFFRACTION7C4 - 108
8X-RAY DIFFRACTION8C109 - 217
9X-RAY DIFFRACTION9C218 - 264
10X-RAY DIFFRACTION10D4 - 109
11X-RAY DIFFRACTION11D110 - 217
12X-RAY DIFFRACTION12D218 - 261

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