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- PDB-5fhn: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in c... -

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Basic information

Entry
Database: PDB / ID: 5fhn
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with (S)-2-Amino-3-(5-(2-(3-methylbenzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at 1.6 A resolution
ComponentsGlutamate receptor 2,Glutamate receptor 2
KeywordsMEMBRANE PROTEIN / Ionotropic glutamate receptor GluA2 / ligand-binding domain
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / 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 ...spine synapse / dendritic spine neck / dendritic spine head / cellular response to amine stimulus / 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 / kainate selective glutamate receptor activity / cellular response to glycine / AMPA glutamate receptor complex / 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 / glutamate-gated receptor activity / regulation of long-term synaptic depression / cytoskeletal protein binding / 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 / ionotropic glutamate receptor binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / synaptic membrane / dendritic shaft / SNARE binding / PDZ domain binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / 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 / signaling receptor activity / presynapse / amyloid-beta binding / growth cone / presynaptic membrane / scaffold protein binding / perikaryon / dendritic spine / chemical synaptic transmission / 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
Chem-5XO / ACETATE ION / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFrydenvang, K. / Kastrup, J.S.
Citation
Journal: J.Med.Chem. / Year: 2016
Title: Tweaking Subtype Selectivity and Agonist Efficacy at (S)-2-Amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)propionic acid (AMPA) Receptors in a Small Series of BnTetAMPA Analogues.
Authors: Wang, S.Y. / Larsen, Y. / Navarrete, C.V. / Jensen, A.A. / Nielsen, B. / Al-Musaed, A. / Frydenvang, K. / Kastrup, J.S. / Pickering, D.S. / Clausen, R.P.
#1: Journal: J. Med. Chem. / Year: 2007
Title: A tetrazolyl-substituted subtype-selective AMPA receptor agonist.
Authors: Vogensen, S.B. / Frydenvang, K. / Greenwood, J.R. / Postorino, G. / Nielsen, B. / Pickering, D.S. / Ebert, B. / Bolcho, U. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. / Johansen, T.N. / ...Authors: Vogensen, S.B. / Frydenvang, K. / Greenwood, J.R. / Postorino, G. / Nielsen, B. / Pickering, D.S. / Ebert, B. / Bolcho, U. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. / Johansen, T.N. / Clausen, R.P. / Krogsgaard-Larsen, P.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Mar 31, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.3Jan 10, 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
Revision 1.4Oct 16, 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,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0247
Polymers29,2791
Non-polymers7466
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.110, 46.380, 46.030
Angle α, β, γ (deg.)90.000, 92.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-654-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate receptor 2,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 Ionotropic glutamate receptor A2 / / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2Ionotropic glutamate receptor A2


Mass: 29278.732 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ligand-binding domain of GluA2. Transmembrane regions genetically removed and replaced with Gly-Thr linker (residues 118-119). Protein consists of UNP residues 413-527 and 653-797, numbering ...Details: ligand-binding domain of GluA2. Transmembrane regions genetically removed and replaced with Gly-Thr linker (residues 118-119). Protein consists of UNP residues 413-527 and 653-797, numbering with signal peptide of 21 residues. The first two residues (Gly, Ala) are cloning remnants.
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491

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Non-polymers , 6 types, 299 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-5XO / (S)-2-Amino-3-(5-(2-(3-methylbenzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid


Mass: 344.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16N6O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 18% PEG4000 0.1 M ammonium sulfate 0.1 M phosphate-citrate buffer pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91949 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91949 Å / Relative weight: 1
ReflectionResolution: 1.6→27.994 Å / Num. all: 38281 / Num. obs: 38281 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.59 Å2 / Rpim(I) all: 0.041 / Rrim(I) all: 0.077 / Rsym value: 0.065 / Net I/av σ(I): 6.469 / Net I/σ(I): 10.7 / Num. measured all: 135601
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.693.50.37321955955360.2310.3733.499.6
1.69-1.793.50.25431857452530.1580.2544.799.8
1.79-1.913.50.1674.41756449480.1040.1676.699.9
1.91-2.073.50.1116.41627345870.0690.1119.4100
2.07-2.263.60.0798.51515342610.0490.07912.2100
2.26-2.533.60.06210.41374538530.0380.06214100
2.53-2.923.60.05511.11219434240.0340.05516.3100
2.92-3.583.60.069.71035929060.0370.0619.4100
3.58-5.063.50.04712.3796622500.030.04721.3100
5.06-27.9943.30.03312421412630.0220.03319.698.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.22data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2p2a

2p2a


Resolution: 1.6→27.994 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 18.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 3898 5.22 %Random
Rwork0.1557 70783 --
obs0.1573 38278 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.33 Å2 / Biso mean: 27.465 Å2 / Biso min: 7.65 Å2
Refinement stepCycle: final / Resolution: 1.6→27.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 90 293 2396
Biso mean--33.93 32.98 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092121
X-RAY DIFFRACTIONf_angle_d1.0092858
X-RAY DIFFRACTIONf_chiral_restr0.06313
X-RAY DIFFRACTIONf_plane_restr0.007355
X-RAY DIFFRACTIONf_dihedral_angle_d11.3541278
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61950.29751460.246125102656100
1.6195-1.640.28761280.236725392667100
1.64-1.66160.27011430.224724982641100
1.6616-1.68430.30031330.212625642697100
1.6843-1.70840.21521610.214924952656100
1.7084-1.73390.23421310.214324752606100
1.7339-1.7610.27361320.199525822714100
1.761-1.78990.21591360.200525342670100
1.7899-1.82070.22481570.192524952652100
1.8207-1.85380.23781250.185525832708100
1.8538-1.88950.22011480.175224512599100
1.8895-1.9280.2151520.165925612713100
1.928-1.96990.18681230.163625102633100
1.9699-2.01570.17571390.157526002739100
2.0157-2.06610.21771260.161524692595100
2.0661-2.1220.18561300.15825862716100
2.122-2.18440.19151500.151325072657100
2.1844-2.25490.17991360.150525452681100
2.2549-2.33540.16391600.152425222682100
2.3354-2.42890.17341360.151725412677100
2.4289-2.53940.22021320.145525002632100
2.5394-2.67320.22591280.145725272655100
2.6732-2.84050.18311390.151425592698100
2.8405-3.05960.14081310.139825332664100
3.0596-3.3670.1641490.141125172666100
3.367-3.85310.16291420.140425692711100
3.8531-4.85040.14831360.124125002636100
4.8504-27.99790.16331490.1522511266099
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)
12.1497-1.06120.91331.95350.24453.53320.03340.20980.2565-0.136-0.16090.0158-0.1789-0.04670.05580.11910.02180.0030.10760.02350.1457-25.63423.6476-0.5552
21.98410.51170.28786.2876-1.4613.17340.11420.40020.147-0.3497-0.06720.1340.01790.0377-0.11940.07750.01980.01840.16290.02280.0568-20.1311-6.2297-4.7821
31.4961-0.64180.18341.3282-0.32443.24640.06290.21440.0741-0.0767-0.0471-0.15590.0920.1714-0.01950.06980.01610.01530.11620.00520.1137-12.3652-9.52730.532
42.8822-0.59550.22261.78760.18662.52130.0021-0.152-0.18250.16790.0798-0.01930.1402-0.1027-0.07090.1153-0.0086-0.01720.06740.00640.1216-15.6678-20.837816.8245
53.61950.1508-1.922.5898-0.512.9685-0.004-0.49270.33310.38020.1522-0.0354-0.3885-0.0999-0.13470.22150.0603-0.01380.1948-0.03940.1118-18.299-7.924919.2988
62.2380.30770.11013.03620.59245.6514-0.03560.19930.2871-0.3690.0193-0.4369-0.20010.3741-0.02610.103-0.01140.06010.18180.03830.2408-8.24262.9469-2.6133
72.54830.10630.01255.1326-0.93986.2557-0.1585-0.17180.0090.37920.01750.0086-0.246-0.2641-0.05270.16290.0478-0.01550.1255-0.05350.2409-20.57017.673413.6107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 47 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 65 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 116 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 187 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 217 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 218 through 243 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 244 through 262 )A0

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