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- PDB-4x48: Crystal structure of GluR2 ligand-binding core -

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Basic information

Entry
Database: PDB / ID: 4x48
TitleCrystal structure of GluR2 ligand-binding core
ComponentsGlutamate receptor 2
KeywordsMEMBRANE PROTEIN / AMPA receptor / allosteric modulator
Function / homology
Function and homology information


spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / 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 / extracellularly glutamate-gated ion channel activity / 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 / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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
GLUTAMIC ACID / Chem-XPF / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsPandit, J.
CitationJournal: J.Med.Chem. / Year: 2015
Title: The Discovery and Characterization of the alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Potentiator N-{(3S,4S)-4-[4-(5-Cyano-2-thienyl)phenoxy]tetrahydrofuran-3- ...Title: The Discovery and Characterization of the alpha-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Potentiator N-{(3S,4S)-4-[4-(5-Cyano-2-thienyl)phenoxy]tetrahydrofuran-3-yl}propane-2-sulfonamide (PF-04958242).
Authors: Shaffer, C.L. / Patel, N.C. / Schwarz, J. / Scialis, R.J. / Wei, Y. / Hou, X.J. / Xie, L. / Karki, K. / Bryce, D.K. / Osgood, S.M. / Hoffmann, W.E. / Lazzaro, J.T. / Chang, C. / McGinnis, D. ...Authors: Shaffer, C.L. / Patel, N.C. / Schwarz, J. / Scialis, R.J. / Wei, Y. / Hou, X.J. / Xie, L. / Karki, K. / Bryce, D.K. / Osgood, S.M. / Hoffmann, W.E. / Lazzaro, J.T. / Chang, C. / McGinnis, D.F. / Lotarski, S.M. / Liu, J. / Obach, R.S. / Weber, M.L. / Chen, L. / Zasadny, K.R. / Seymour, P.A. / Schmidt, C.J. / Hajos, M. / Hurst, R.S. / Pandit, J. / O'Donnell, C.J.
History
DepositionDec 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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 / diffrn_radiation_wavelength / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,58513
Polymers91,0323
Non-polymers1,55310
Water12,647702
1
A: Glutamate receptor 2
C: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5718
Polymers60,6882
Non-polymers8836
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-41 kcal/mol
Surface area23060 Å2
MethodPISA
2
B: Glutamate receptor 2
hetero molecules

B: Glutamate receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,02910
Polymers60,6882
Non-polymers1,3418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2430 Å2
ΔGint-87 kcal/mol
Surface area23220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.759, 164.965, 47.363
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsBiological unit is a dimer. The asymmetric unit has 3 chains (A,B,C) of which chains A and C make one NCS-related dimer, and chain B makes a dimer with a crystallographic two-fold related partner.

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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: 30343.840 Da / Num. of mol.: 3 / Fragment: Ligand binding domain, engineered single chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19491
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-XPF / N-{(3S,4S)-4-[4-(5-cyanothiophen-2-yl)phenoxy]tetrahydrofuran-3-yl}propane-2-sulfonamide


Mass: 392.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N2O4S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: The protein solution contained 7 mg/ml GluR2-S1S2J, 10mM (S)-Glu, 10mM HEPES (pH 7.5), 20mM NaCl and 1mM EDTA. Compound was added to a final concentration of 150micromolar from a 30mM DMSO ...Details: The protein solution contained 7 mg/ml GluR2-S1S2J, 10mM (S)-Glu, 10mM HEPES (pH 7.5), 20mM NaCl and 1mM EDTA. Compound was added to a final concentration of 150micromolar from a 30mM DMSO stock. To this solution, an equal amount of reservoir solution containing 10% PEG 8000, 0.1 M ZnAc and 0.1M NaAc, pH 5.5 was added, and 2microlitre drops of this mixture were allowed to equilibrate by vapor diffusion over a 1mL reservoir. Crystals appeared in the drops in 3-5 days.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.886→164.965 Å / Num. all: 69522 / Num. obs: 69522 / % possible obs: 94.8 % / Redundancy: 5.4 % / Biso Wilson estimate: 31.53 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.088 / Rsym value: 0.074 / Net I/av σ(I): 5.979 / Net I/σ(I): 13.7 / Num. measured all: 372534
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
1.89-1.992.20.3921.81668074870.2930.392271.9
1.99-2.112.80.2362.92638793210.1590.2363.793.9
2.11-2.254.30.16744049794310.0970.1676.999.5
2.25-2.436.40.1474.45650287900.0690.14710.6100
2.43-2.676.70.1135.55449781290.0520.11314.4100
2.67-2.986.90.0926.15092174070.0420.09218.7100
2.98-3.446.90.0787.14531665650.0350.07823.6100
3.44-4.226.80.0668.73778455860.0290.06627100
4.22-5.966.70.0589.52946344290.0260.05827.8100
5.96-164.9656.10.052121448723770.0240.05226.793.4

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Processing

Software
NameVersionClassification
SCALA3.3.9data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.15data extraction
BUSTER-TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LZ5

4lz5


Resolution: 1.89→27.67 Å / Cor.coef. Fo:Fc: 0.9508 / Cor.coef. Fo:Fc free: 0.9426 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 3546 5.13 %RANDOM
Rwork0.1734 ---
obs0.1747 69180 94.8 %-
Displacement parametersBiso max: 115.96 Å2 / Biso mean: 37.53 Å2 / Biso min: 14.27 Å2
Baniso -1Baniso -2Baniso -3
1--4.5672 Å20 Å20 Å2
2---2.7214 Å20 Å2
3---7.2885 Å2
Refine analyzeLuzzati coordinate error obs: 0.214 Å
Refinement stepCycle: final / Resolution: 1.89→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6035 0 113 702 6850
Biso mean--29.81 48.3 -
Num. residues----772
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2222SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes141HARMONIC2
X-RAY DIFFRACTIONt_gen_planes898HARMONIC5
X-RAY DIFFRACTIONt_it6257HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion804SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7528SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6257HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8421HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion15.64
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2554 209 5.98 %
Rwork0.2164 3286 -
all0.2188 3495 -
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)
11.1861-0.3873-0.23951.36990.38331.6983-0.0470.0196-0.0012-0.0218-0.0162-0.03770.10740.29470.0632-0.05590.0209-0.0171-0.00840.034-0.043676.769930.049541.8267
20.87850.08940.35171.54730.55311.2464-0.0215-0.0094-0.03060.02980.00310.02350.12010.120.0185-0.06330.03040.0191-0.06390.0172-0.036166.501570.275851.3508
31.8754-0.24410.14940.9807-0.27471.8269-0.0480.1013-0.0369-0.09260.0294-0.0243-0.0303-0.16650.0186-0.0374-0.0366-0.0057-0.0413-0.0401-0.050247.040923.485141.5787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|393 - A|508 A|632 - A|773 }A393 - 508
2X-RAY DIFFRACTION1{ A|393 - A|508 A|632 - A|773 }A632 - 773
3X-RAY DIFFRACTION2{ B|394 - B|508 B|632 - B|773 }B394 - 508
4X-RAY DIFFRACTION2{ B|394 - B|508 B|632 - B|773 }B632 - 773
5X-RAY DIFFRACTION3{ C|394 - C|508 C|632 - C|773 }C394 - 508
6X-RAY DIFFRACTION3{ C|394 - C|508 C|632 - C|773 }C632 - 773

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