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

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Basic information

Entry
Database: PDB / ID: 5fhm
TitleCrystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with (S)-2-Amino-3-(5-(2-(3-(aminomethyl)benzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at resolution 1.55 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 / 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 / extracellularly glutamate-gated ion channel activity ...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 / extracellularly glutamate-gated ion channel activity / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / 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 / 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 / ionotropic glutamate receptor binding / somatodendritic compartment / dendrite membrane / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein 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
Chem-5XP / ACETATE ION / : / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKastrup, J.S. / Frydenvang, K. / Al-musaed, A.
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 1.1Mar 23, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 2,Glutamate receptor 2
B: Glutamate receptor 2,Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,36224
Polymers58,5572
Non-polymers1,80422
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-85 kcal/mol
Surface area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.510, 94.056, 96.112
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,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


Mass: 29278.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions genetically removed and replaced with Gly-Thr linker (residues 118-119). Protein consists of ...Details: Protein crystallized is the extracellular 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 , 7 types, 708 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-5XP / (2~{S})-3-[5-[2-[[3-(aminomethyl)phenyl]methyl]-1,2,3,4-tetrazol-5-yl]-3-oxidanyl-1,2-oxazol-4-yl]-2-azanyl-propanoic acid


Mass: 359.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N7O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG4000 lithium sulfate sodium acetate buffer pH 5.5
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→48.06 Å / Num. all: 82889 / Num. obs: 82889 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 12.85 Å2 / Rpim(I) all: 0.021 / Rrim(I) all: 0.061 / Rsym value: 0.058 / Net I/av σ(I): 11.075 / Net I/σ(I): 23.1 / Num. measured all: 678969
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
1.55-1.638.10.4071.997380119500.1510.4075.2100
1.63-1.738.20.282.792748113360.1040.287.2100
1.73-1.858.20.1844.287599106710.0680.18410.2100
1.85-28.20.1156.68191899570.0430.11515.8100
2-2.198.20.07210.37561391660.0270.07223.7100
2.19-2.458.30.056136891783360.0210.05629.6100
2.45-2.838.30.047156111073870.0170.04736100
2.83-3.478.20.03618.25192863030.0130.03649.3100
3.47-4.98.10.02723.84016649450.010.02763.2100
4.9-48.0567.60.02524.22159028380.010.02553.199.5

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P2A (molB)

2p2a


Resolution: 1.55→47.028 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1585 7958 5.01 %Random
Rwork0.137 150914 --
obs0.1381 82806 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.42 Å2 / Biso mean: 20.2072 Å2 / Biso min: 5.35 Å2
Refinement stepCycle: final / Resolution: 1.55→47.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 201 695 4936
Biso mean--40.11 29.21 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094318
X-RAY DIFFRACTIONf_angle_d1.0225814
X-RAY DIFFRACTIONf_chiral_restr0.058634
X-RAY DIFFRACTIONf_plane_restr0.007723
X-RAY DIFFRACTIONf_dihedral_angle_d11.3592625
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.56760.25582700.192150315301100
1.5676-1.58610.19742760.182650145290100
1.5861-1.60540.18092530.174650675320100
1.6054-1.62570.17162570.170350105267100
1.6257-1.64710.18292530.167350795332100
1.6471-1.66970.20512580.165649745232100
1.6697-1.69350.18882730.161350555328100
1.6935-1.71880.20052540.158550405294100
1.7188-1.74570.182420.148950835325100
1.7457-1.77430.17282390.144150375276100
1.7743-1.80490.14422770.144550145291100
1.8049-1.83770.17983020.143850315333100
1.8377-1.87310.16462400.145150335273100
1.8731-1.91130.16482510.141850385289100
1.9113-1.95290.16442440.135551035347100
1.9529-1.99830.15392560.135750035259100
1.9983-2.04830.14822610.128250455306100
2.0483-2.10360.14292740.128550045278100
2.1036-2.16550.15942390.125650555294100
2.1655-2.23540.13173070.121250175324100
2.2354-2.31530.16122990.121949865285100
2.3153-2.4080.16752940.126450125306100
2.408-2.51760.15872650.131450135278100
2.5176-2.65030.12832790.12750125291100
2.6503-2.81640.15812810.124550445325100
2.8164-3.03380.18092600.134450065266100
3.0338-3.3390.15012840.1350195303100
3.339-3.8220.12752550.125150535308100
3.822-4.81450.12862510.118950515302100
4.8145-47.04960.19242640.17214985524999
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)
13.0141-0.54050.29821.92610.10571.69250.02660.07510.1399-0.0353-0.0357-0.2738-0.01770.0674-0.01260.0686-0.00130.00890.06650.01430.09726.4977-2.930630.0996
20.52470.02350.25290.57020.32521.176-0.0233-0.0452-0.03580.0540.01550.0060.0771-0.0141-0.00340.05890.00620.01590.0610.01650.0775-8.2288-11.298129.6542
31.86740.3306-0.33781.96580.58521.557-0.0180.0521-0.0381-0.0532-0.02850.06060.03550.02540.04330.0751-0.00310.00430.07870.0070.0588-11.4002-18.031614.4539
41.3808-0.0455-0.07362.14040.5061.2992-0.03840.12370.077-0.2013-0.0204-0.1387-0.05740.10340.01370.07990.01980.00960.10780.02490.0962-4.94112.813126.8765
51.97250.28380.16621.7480.16641.1122-0.0180.0226-0.0502-0.0069-0.01330.2743-0.0388-0.10950.03480.07990.01620.01330.0898-0.00380.122-37.27798.09929.3236
60.46540.055-0.38890.7573-0.2061.22280.006-0.01240.01810.0345-0.01630.0152-0.11350.007-0.00470.0650.0071-0.01450.0668-0.00980.0719-22.114413.271228.8246
71.74720.53280.73972.3228-0.18281.2896-0.0017-0.02640.0576-0.0896-0.06720.0181-0.0396-0.04880.06350.08050.01540.0030.0964-0.00690.0532-18.136821.133912.9807
80.76140.08610.56851.9227-0.35562.8386-0.05950.0124-0.1171-0.03170.02820.09610.0323-0.130.00750.0330.0070.01430.0748-0.01560.1135-27.19770.097825.7389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 47 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 123 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 217 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 261 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 65 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 66 through 123 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 124 through 217 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 218 through 262 )B0

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