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- PDB-4q30: Nitrowillardiine bound to the ligand binding domain of GluA2 at pH 3.5 -

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Basic information

Entry
Database: PDB / ID: 4q30
TitleNitrowillardiine bound to the ligand binding domain of GluA2 at pH 3.5
ComponentsGlutamate receptor 2 CHIMERIC PROTEIN
KeywordsTRANSPORT PROTEIN / glutamate receptor / GluA2 / GluR2 / AMPA receptor / LBD / neurotransmitter receptor / nitrowillardiine
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 / immunoglobulin binding ...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 / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / ionotropic glutamate receptor binding / presynaptic active zone membrane / extracellular ligand-gated monoatomic ion channel activity / somatodendritic compartment / glutamate-gated calcium ion channel activity / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / establishment of protein localization / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / synaptic vesicle membrane / synaptic vesicle / presynapse / signaling receptor activity / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / dendritic spine / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / axon / neuronal cell body / synapse / dendrite / protein-containing complex binding / protein kinase 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-NWD / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsAhmed, A.H. / Oswald, R.E.
CitationJournal: Biochemistry / Year: 2014
Title: Thermodynamics and mechanism of the interaction of willardiine partial agonists with a glutamate receptor: implications for drug development.
Authors: Martinez, M. / Ahmed, A.H. / Loh, A.P. / Oswald, R.E.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 26, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 1.3Sep 20, 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_auth_seq_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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Glutamate receptor 2 CHIMERIC PROTEIN
D: Glutamate receptor 2 CHIMERIC PROTEIN
F: Glutamate receptor 2 CHIMERIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,48111
Polymers86,4223
Non-polymers1,0608
Water14,430801
1
B: Glutamate receptor 2 CHIMERIC PROTEIN
D: Glutamate receptor 2 CHIMERIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3658
Polymers57,6152
Non-polymers7506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-85 kcal/mol
Surface area23180 Å2
MethodPISA
2
F: Glutamate receptor 2 CHIMERIC PROTEIN
hetero molecules

F: Glutamate receptor 2 CHIMERIC PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2346
Polymers57,6152
Non-polymers6194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554x,-y,-z-11
Buried area1970 Å2
ΔGint-111 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.797, 113.270, 164.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Glutamate receptor 2 CHIMERIC PROTEIN / 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: 28807.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Glur2, Gria2, Gria2; GluA2 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19491
#2: Chemical ChemComp-NWD / 3-(5-nitro-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alanine / nitrowillardiine


Type: L-peptide linking / Mass: 244.162 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N4O6
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 801 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN THIS PROTEIN PART OF THE TRANSMEMBRANE ION CHANNEL HAS BEEN REMOVED AND REPLACED BY A 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 3.5, 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: Feb 20, 2013
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: 2.03→50 Å / Num. all: 412588 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 25.354
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 4 / Rsym value: 0.751 / % possible all: 97.7

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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 3RTW

3rtw


Resolution: 2.03→44.037 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 1944 3.43 %RANDOM
Rwork0.1858 ---
obs0.1873 56635 96.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.14 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3414 Å20 Å20 Å2
2--2.7992 Å2-0 Å2
3---1.5422 Å2
Refinement stepCycle: LAST / Resolution: 2.03→44.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 56 801 6857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076165
X-RAY DIFFRACTIONf_angle_d1.0578299
X-RAY DIFFRACTIONf_dihedral_angle_d14.6592285
X-RAY DIFFRACTIONf_chiral_restr0.072914
X-RAY DIFFRACTIONf_plane_restr0.0041034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0289-2.07970.23961250.19153455X-RAY DIFFRACTION86
2.0797-2.13590.25391250.19063711X-RAY DIFFRACTION94
2.1359-2.19870.24261360.19543736X-RAY DIFFRACTION94
2.1987-2.26970.25981360.18763789X-RAY DIFFRACTION94
2.2697-2.35080.25481330.20073824X-RAY DIFFRACTION96
2.3508-2.44490.26391390.20053826X-RAY DIFFRACTION96
2.4449-2.55620.261420.19633907X-RAY DIFFRACTION97
2.5562-2.69090.26031390.19233926X-RAY DIFFRACTION98
2.6909-2.85950.23381400.19353969X-RAY DIFFRACTION98
2.8595-3.08020.20841430.18914004X-RAY DIFFRACTION99
3.0802-3.39010.19791440.17074053X-RAY DIFFRACTION99
3.3901-3.88040.20821450.16454083X-RAY DIFFRACTION100
3.8804-4.88790.17031460.15424128X-RAY DIFFRACTION100
4.8879-44.04720.26911510.19934280X-RAY DIFFRACTION99

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