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- PDB-3m3k: Ligand binding domain (S1S2) of GluA3 (flop) -

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Basic information

Entry
Database: PDB / ID: 3m3k
TitleLigand binding domain (S1S2) of GluA3 (flop)
ComponentsGlutamate receptor 3
KeywordsTRANSPORT PROTEIN / glutamate receptor / GluA3 / GluR3 / AMPA receptor / neurotransmitter receptor / S1S2
Function / homology
Function and homology information


chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / monoatomic ion transmembrane transport / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / amyloid-beta binding / perikaryon / chemical synaptic transmission / postsynaptic membrane / dendritic spine / postsynaptic density / dendrite / neuronal cell body / glutamatergic synapse / protein-containing complex / 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 / Glutamate receptor 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.793 Å
AuthorsAhmed, A.H. / Ptak, C.P. / Oswald, R.E.
CitationJournal: Biochemistry / Year: 2010
Title: Molecular mechanism of flop selectivity and subsite recognition for an AMPA receptor allosteric modulator: structures of GluA2 and GluA3 in complexes with PEPA.
Authors: Ahmed, A.H. / Ptak, C.P. / Oswald, R.E.
History
DepositionMar 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.3Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_label_asym_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 / _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 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 3
C: Glutamate receptor 3
E: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,61410
Polymers86,9113
Non-polymers7037
Water14,430801
1
A: Glutamate receptor 3
C: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4317
Polymers57,9412
Non-polymers4905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-73 kcal/mol
Surface area22350 Å2
2
E: Glutamate receptor 3
hetero molecules

E: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3666
Polymers57,9412
Non-polymers4254
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554x,-y,-z-11
Buried area1990 Å2
ΔGint-69 kcal/mol
Surface area22320 Å2
Unit cell
Length a, b, c (Å)46.028, 110.329, 161.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-753-

HOH

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Components

#1: Protein Glutamate receptor 3 / / GluR-3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / AMPA 3 / AMPA-selective glutamate receptor 3


Mass: 28970.402 Da / Num. of mol.: 3 / Fragment: UNP residues 417-530, 658-799
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria3, Glur3 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19492
#2: Chemical ChemComp-GLU / GLUTAMIC ACID / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 801 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14-15% PEG 8000, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 23, 2008
RadiationMonochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.793→50 Å / Num. obs: 69379 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 34.342
Reflection shellResolution: 1.793→1.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3.333 / Num. unique all: 2772 / Rsym value: 0.246 / % possible all: 73.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementStarting model: PDB entry 3DLN

3dln


Resolution: 1.793→28.732 Å / SU ML: 0.24 / σ(F): 0.46 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 2000 2.88 %
Rwork0.2012 --
obs0.2023 69379 88.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.891 Å2 / ksol: 0.419 e/Å3
Refinement stepCycle: LAST / Resolution: 1.793→28.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6095 0 34 801 6930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096210
X-RAY DIFFRACTIONf_angle_d1.268353
X-RAY DIFFRACTIONf_dihedral_angle_d14.9932303
X-RAY DIFFRACTIONf_chiral_restr0.071922
X-RAY DIFFRACTIONf_plane_restr0.0051049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.793-1.83830.2937570.2111929X-RAY DIFFRACTION36
1.8383-1.8880.27271080.20073650X-RAY DIFFRACTION69
1.888-1.94350.24961280.20014273X-RAY DIFFRACTION80
1.9435-2.00620.2221450.18444892X-RAY DIFFRACTION91
2.0062-2.07790.24411490.18775017X-RAY DIFFRACTION94
2.0779-2.16110.24681500.1825052X-RAY DIFFRACTION95
2.1611-2.25940.23341520.19175126X-RAY DIFFRACTION96
2.2594-2.37850.2511540.19375195X-RAY DIFFRACTION97
2.3785-2.52740.23771550.20095243X-RAY DIFFRACTION97
2.5274-2.72240.23811580.19585292X-RAY DIFFRACTION98
2.7224-2.99610.21981590.20125362X-RAY DIFFRACTION99
2.9961-3.42910.23911600.18935419X-RAY DIFFRACTION99
3.4291-4.31790.21651630.17885465X-RAY DIFFRACTION99
4.3179-28.73520.25441620.23495464X-RAY DIFFRACTION95

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