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- PDB-3rt8: Chlorowillardiine bound to the ligand binding domain of GluA3 -

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Basic information

Entry
Database: PDB / ID: 3rt8
TitleChlorowillardiine bound to the ligand binding domain of GluA3
ComponentsGlutamate receptor 3
KeywordsTRANSPORT PROTEIN / glutamate receptor / GluR3 / AMPA receptor / S1S2 / neurotransmitter receptor
Function / homology
Function and homology information


Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / protein heterotetramerization / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex ...Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / protein heterotetramerization / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate-gated receptor activity / synaptic cleft / response to fungicide / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendritic shaft / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / long-term synaptic potentiation / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / amyloid-beta binding / perikaryon / postsynaptic membrane / protein homotetramerization / dendritic spine / postsynaptic density / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex / 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-CWD / Glutamate receptor 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.426 Å
AuthorsAhmed, A.H. / Oswald, R.E.
CitationJournal: Mol.Pharmacol. / Year: 2011
Title: Mechanisms of Modal Activation of GluA3 Receptors.
Authors: Poon, K. / Ahmed, A.H. / Nowak, L.M. / Oswald, R.E.
History
DepositionMay 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.3Sep 13, 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_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 / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2553
Polymers28,9561
Non-polymers2992
Water2,702150
1
A: Glutamate receptor 3
hetero molecules

A: Glutamate receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5116
Polymers57,9132
Non-polymers5984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area1500 Å2
ΔGint-9 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.325, 49.157, 140.478
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Glutamate receptor 3 / GluA3 / GluR-3 / AMPA-selective glutamate receptor 3 / GluR-C / GluR-K3 / Glutamate receptor ...GluA3 / GluR-3 / AMPA-selective glutamate receptor 3 / GluR-C / GluR-K3 / Glutamate receptor ionotropic / AMPA 3


Mass: 28956.418 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GluA3, Glur3, Gria3 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P19492
#2: Chemical ChemComp-CWD / 3-(5-chloro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine / chlorowillardiine


Type: L-peptide linking / Mass: 233.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8ClN3O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN IS NATURAL ISOFORM FLIP (P19492-2). PROTEIN FRAGMENT CONSISTS OF UNP RESIDUES 417-530 AND ...PROTEIN IS NATURAL ISOFORM FLIP (P19492-2). PROTEIN FRAGMENT CONSISTS OF UNP RESIDUES 417-530 AND UNP RESIDUES 658-799 CONNECTED BY AN ENGINEERED 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: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14-15% PEG8000, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, 0.1 M sodium cacodylate, 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
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 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: 2.4→50 Å / Num. all: 10646 / Num. obs: 10645 / % possible obs: 79.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 12.333
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 0.249 / Rsym value: 0.03634 / % possible all: 81.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DLN

3dln


Resolution: 2.426→33.796 Å / SU ML: 0.43 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.13 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 1040 9.94 %RANDOM
Rwork0.223 ---
obs0.2285 10462 77.04 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.8 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0342 Å2-0 Å20 Å2
2---5.734 Å2-0 Å2
3---2.6998 Å2
Refinement stepCycle: LAST / Resolution: 2.426→33.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 16 150 2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062086
X-RAY DIFFRACTIONf_angle_d0.9342808
X-RAY DIFFRACTIONf_dihedral_angle_d15.263778
X-RAY DIFFRACTIONf_chiral_restr0.062308
X-RAY DIFFRACTIONf_plane_restr0.005349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4258-2.55360.33421300.26311251X-RAY DIFFRACTION73
2.5536-2.71360.32811580.25651461X-RAY DIFFRACTION85
2.7136-2.9230.3171650.24731479X-RAY DIFFRACTION86
2.923-3.21690.34031690.24551472X-RAY DIFFRACTION87
3.2169-3.68190.26331530.22921343X-RAY DIFFRACTION79
3.6819-4.63690.20411030.169930X-RAY DIFFRACTION69
4.6369-33.79910.23141620.19471486X-RAY DIFFRACTION79

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